Mock Version: 2.11
Mock Version: 2.11
Mock Version: 2.11
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/eln-build-28771619-3885803/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f8d3cc18c10>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1623024000
Wrote: /builddir/build/SRPMS/R-4.1.0-1.eln112.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/eln-build-28771619-3885803/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f8d3cc18c10>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1623024000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.2XcchT
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf R-4.1.0
+ /usr/bin/gzip -dc /builddir/build/SOURCES/R-4.1.0.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd R-4.1.0
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):
+ echo 'Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .fixpath --fuzz=0
patching file src/scripts/javareconf.in
Hunk #1 succeeded at 79 (offset 1 line).
+ cat
+ chmod +x /builddir/build/BUILD/R-4.1.0/R-prov
+ cat
+ chmod +x /builddir/build/BUILD/R-4.1.0/R-req
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.H0VK3j
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-4.1.0
+ echo 'R_LIBS_SITE=${R_LIBS_SITE-'\''/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library'\''}'
+ export R_RD4PDF=times,hyper
+ R_RD4PDF=times,hyper
+ sed -i 's|inconsolata,||g' etc/Renviron.in
+ export R_PDFVIEWER=/usr/bin/xdg-open
+ R_PDFVIEWER=/usr/bin/xdg-open
+ export R_PRINTCMD=lpr
+ R_PRINTCMD=lpr
+ export R_BROWSER=/usr/bin/xdg-open
+ R_BROWSER=/usr/bin/xdg-open
+ case "x86_64" in
+ export 'CC=gcc -m64'
+ CC='gcc -m64'
+ export 'CXX=g++ -m64'
+ CXX='g++ -m64'
+ export 'F77=gfortran -m64'
+ F77='gfortran -m64'
+ export 'FC=gfortran -m64'
+ FC='gfortran -m64'
+ export 'FCFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC='gcc -m64'
+ export CC
+ CXX='g++ -m64'
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
+ tee CONFIGURE.log
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup	2021-05-10 22:15:53.000000000 +0000
+++ ./configure	2021-07-26 04:22:28.636729607 +0000
@@ -2557,7 +2557,7 @@
 #ifdef __cplusplus
 extern "C"
 #endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
 /* The GNU C library defines this for functions which it implements
     to always fail with ENOSYS.  Some functions are actually named
     something starting with __ and the normal name is an alias.  */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup	2021-07-26 04:22:28.636729607 +0000
+++ ./configure	2021-07-26 04:22:28.675732947 +0000
@@ -48717,10 +48717,7 @@
   exit (sig != SIGFPE);
 }
 
-int x = 1;
-int y = 0;
-int z;
-int nan;
+volatile int x = 1; volatile int y = 0; volatile int z, nan;
 
 int main ()
 {
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup	2021-07-26 04:22:28.675732947 +0000
+++ ./configure	2021-07-26 04:22:28.699735003 +0000
@@ -10594,7 +10594,7 @@
 # Transform an extracted symbol line into a proper C declaration.
 # Some systems (esp. on ia64) link data and code symbols differently,
 # so use this general approach.
-lt_cv_sys_global_symbol_to_cdecl="sed -n"\
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
 $lt_cdecl_hook\
 " -e 's/^T .* \(.*\)$/extern int \1();/p'"\
 " -e 's/^$symcode$symcode* .* \(.*\)$/extern char \1;/p'"
@@ -53387,7 +53387,7 @@
 compiler='`$ECHO "$compiler" | $SED "$delay_single_quote_subst"`'
 GCC='`$ECHO "$GCC" | $SED "$delay_single_quote_subst"`'
 lt_cv_sys_global_symbol_pipe='`$ECHO "$lt_cv_sys_global_symbol_pipe" | $SED "$delay_single_quote_subst"`'
-lt_cv_sys_global_symbol_to_cdecl='`$ECHO "$lt_cv_sys_global_symbol_to_cdecl" | $SED "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
 lt_cv_sys_global_symbol_to_import='`$ECHO "$lt_cv_sys_global_symbol_to_import" | $SED "$delay_single_quote_subst"`'
 lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "$lt_cv_sys_global_symbol_to_c_name_address" | $SED "$delay_single_quote_subst"`'
 lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $SED "$delay_single_quote_subst"`'
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./tools/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./tools/config.guess
++ basename ./tools/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./tools/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './tools/config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./tools/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./tools/config.sub
++ basename ./tools/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./tools/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './tools/config.sub'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
+ for i in $(find . -name ltmain.sh)
+ /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./tools/ltmain.sh
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-system-tre --with-system-valgrind-headers --with-lapack --with-blas --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh --enable-R-shlib --enable-prebuilt-html --enable-R-profiling --enable-memory-profiling MAKEINFO=texi2any rdocdir=/usr/share/doc/R rincludedir=/usr/include/R rsharedir=/usr/share/R
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /usr/bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /usr/bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /usr/bin/gtar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... /usr/bin/texi2any
checking whether texi2any version is at least 5.1... yes
checking for ginstall-info... no
checking for install-info... /usr/sbin/install-info
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /usr/bin/bzip2
using default browser ... /usr/bin/xdg-open
checking for /usr/bin/xdg-open... /usr/bin/xdg-open
checking for working aclocal... found
checking for working autoconf... found
checking for working autoheader... found
checking for bison... no
checking for byacc... no
checking for yacc... no
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for x86_64-redhat-linux-gnu-gcc... gcc -m64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 accepts -g... yes
checking for gcc -m64 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m64 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc -m64 needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... gcc -m64 -E
looking for a modern Fortran compiler
checking for x86_64-redhat-linux-gnu-gfortran... gfortran -m64
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran -m64 accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -m64 accepts -g... yes
checking whether g++ -m64 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -m64 -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -m64 accepts -fvisibility... yes
checking whether g++ -m64 accepts -fvisibility... yes
checking whether gfortran -m64 accepts -fvisibility... yes
checking for x86_64-redhat-linux-gnu-gcc... no
checking for x86_64-redhat-linux-gnu-objcc... no
checking for x86_64-redhat-linux-gnu-objc... no
checking for x86_64-redhat-linux-gnu-cc... no
checking for x86_64-redhat-linux-gnu-CC... no
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking whether g++ -m64 can compile ObjC++... no
checking whether  can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc -m64... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-redhat-linux-gnu file names to x86_64-redhat-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-redhat-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-redhat-linux-gnu-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-redhat-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-redhat-linux-gnu-ar... (cached) ar
checking for archiver @FILE support... @
checking for x86_64-redhat-linux-gnu-strip... no
checking for strip... strip
checking for x86_64-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc -m64 object... ./configure: line 10600:  -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p': No such file or directory
ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for x86_64-redhat-linux-gnu-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -m64 supports -fno-rtti -fno-exceptions... no
checking for gcc -m64 option to produce PIC... -fPIC -DPIC
checking if gcc -m64 PIC flag -fPIC -DPIC works... yes
checking if gcc -m64 static flag -static works... no
checking if gcc -m64 supports -c -o file.o... yes
checking if gcc -m64 supports -c -o file.o... (cached) yes
checking whether the gcc -m64 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -m64 -E
checking for ld used by g++ -m64... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -m64 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -m64 option to produce PIC... -fPIC -DPIC
checking if g++ -m64 PIC flag -fPIC -DPIC works... yes
checking if g++ -m64 static flag -static works... no
checking if g++ -m64 supports -c -o file.o... yes
checking if g++ -m64 supports -c -o file.o... (cached) yes
checking whether the g++ -m64 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran -m64 option to produce PIC... -fPIC
checking if gfortran -m64 PIC flag -fPIC works... yes
checking if gfortran -m64 static flag -static works... no
checking if gfortran -m64 supports -c -o file.o... yes
checking if gfortran -m64 supports -c -o file.o... (cached) yes
checking whether the gfortran -m64 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for tilde_expand_word... yes
checking whether rl_completion_matches exists and is declared... yes
checking whether rl_resize_terminal exists and is declared... yes
checking whether rl_sort_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for dlfcn.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
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checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking stdalign.h usability... yes
checking stdalign.h presence... yes
checking for stdalign.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for gcc -m64 option to accept ISO C99... none needed
checking for gcc -m64 option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking for C stack direction... down
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc -m64 supports -c -o FILE.lo... yes
checking for gcc -m64 option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran -m64... -v
checking for Fortran libraries of gfortran -m64...  -L/usr/lib/gcc/x86_64-redhat-linux/11 -L/usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/11/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from gcc -m64... -v
checking for C libraries of gcc -m64...  -L/usr/lib/gcc/x86_64-redhat-linux/11 -L/usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/11/../../.. -lgcc_s
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether gfortran -m64 appends underscores to external names... yes
checking whether gfortran -m64 appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran -m64 and gcc -m64 agree on int and double... yes
checking whether gfortran -m64 and gcc -m64 agree on double complex... yes
checking for gfortran -m64 option to support OpenMP... -fopenmp
checking whether g++ -m64 accepts -M for generating dependencies... yes
checking whether we can compute ObjC Make dependencies... no
checking if need -fno-optimize-sibling-calls for gfortran... yes
checking for type of 'hidden' Fortran character lengths... size_t
checking for xmkmf... no
checking whether g++ -m64  supports C++11 features with -std=gnu++11... yes
checking whether g++ -m64  supports C++14 features with -std=gnu++14... yes
checking whether g++ -m64  supports C++17 features with -std=gnu++17... yes
checking whether g++ -m64  supports C++20 features with -std=gnu++20... yes
checking for g++ -m64 -std=gnu++14 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for __cospi... no
checking for __sinpi... no
checking for __tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... no
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwnam exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether getline exists and is declared... yes
checking whether select exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether setrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking whether utimensat exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for dladdr... yes
checking for dlsym... yes
checking whether dladdr is declared... yes
checking whether dlsym is declared... yes
checking whether RTLD_DEFAULT is declared... yes
checking whether RTLD_NEXT is declared... yes
checking thread.h usability... no
checking thread.h presence... no
checking for thread.h... no
checking whether thr_stksegment exists and is declared... no
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... no
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... no
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking for working ctanh... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
configure: searching for an external BLAS
configure: searching for BLAS in default libraries
checking for dgemm_... no
configure: searching for OpenBLAS
checking for sgemm_ in -lopenblas... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking whether iconv accepts "CP1252"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration... 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking whether wcwidth exists and is declared... yes
checking whether wcswidth exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... yes
checking X11/Xmu/Atoms.h presence... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh
checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking rpc/types.h usability... no
checking rpc/types.h presence... no
checking for rpc/types.h... no
checking tirpc/rpc/types.h usability... no
checking tirpc/rpc/types.h presence... no
checking for tirpc/rpc/types.h... no
checking for XDR support... no
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support suffices... yes
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
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checking if lzma version >= 5.0.3... yes
checking pcre2.h usability... yes
checking pcre2.h presence... yes
checking for pcre2.h... yes
checking for pcre2_compile_8 in -lpcre2-8... yes
checking if PCRE2 has Unicode support... yes
checking whether PCRE support suffices... yes
checking for tre_regncompb in -ltre... yes
checking tre/tre.h usability... yes
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checking for tre/tre.h... yes
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.78.0
checking curl/curl.h usability... yes
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checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.28.0... yes
checking if libcurl supports https... yes
checking if pkg-config knows about libjpeg... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if pkg-config knows about libpng... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking if pkg-config knows about libtiff... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for paperconf... /usr/bin/paperconf
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for gfortran -m64 option to support OpenMP... (cached) -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for x86_64-redhat-linux-gnu-ranlib... ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by gcc -m64... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached) 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... no
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory
checking whether OpenMP SIMD reduction is supported... yes
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
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configure: WARNING: unrecognized options: --disable-dependency-tracking
R is now configured for x86_64-redhat-linux-gnu
  Source directory:            .
  Installation directory:      /usr
  C compiler:                  gcc -m64  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  Fortran fixed-form compiler: gfortran -m64 -fno-optimize-sibling-calls -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules
  Default C++ compiler:        g++ -m64 -std=gnu++14  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  C++11 compiler:              g++ -m64 -std=gnu++11  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  C++14 compiler:              g++ -m64 -std=gnu++14  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  C++17 compiler:              g++ -m64 -std=gnu++17  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  C++20 compiler:              g++ -m64 -std=gnu++20  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  Fortran free-form compiler:  gfortran -m64 -fno-optimize-sibling-calls -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
  Obj-C compiler:	        
  Interfaces supported:        X11, tcltk
  External libraries:          pcre2, readline, BLAS(OpenBLAS), LAPACK(in blas), tre, curl
  Additional capabilities:     PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:             shared R library, R profiling, memory profiling, static HTML
  Capabilities skipped:        
  Options not enabled:         shared BLAS
  Recommended packages:        yes
+ cat CONFIGURE.log
+ grep -A30 'R is now' -
+ make V=1
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/m4'
make[1]: Nothing to be done for 'R'.
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/m4'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/tools'
make[1]: Nothing to be done for 'R'.
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tools'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/doc'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/doc/html'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/doc/html'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/doc/manual'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/doc/manual'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/doc'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/etc'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/etc'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/share'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/share'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/scripts'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/scripts'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/include'
mkdir -p -- ../../include
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/include/R_ext'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/include'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/extra'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/extra/xdr'
making xdr.d from xdr.c
making xdr_float.d from xdr_float.c
making xdr_mem.d from xdr_mem.c
making xdr_stdio.d from xdr_stdio.c
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/extra/xdr'
gcc -m64 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -fvisibility=hidden -c xdr.c -o xdr.o
gcc -m64 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -fvisibility=hidden -c xdr_float.c -o xdr_float.o
gcc -m64 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -fvisibility=hidden -c xdr_mem.c -o xdr_mem.o
gcc -m64 -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -fvisibility=hidden -c xdr_stdio.c -o xdr_stdio.o
ar -cr libxdr.a xdr.o xdr_float.o xdr_mem.o xdr_stdio.o
ranlib libxdr.a
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/extra/xdr'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/extra/xdr'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/extra'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/appl'
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/appl'
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c integrate.c -o integrate.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c interv.c -o interv.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c maxcol.c -o maxcol.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c optim.c -o optim.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pretty.c -o pretty.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c uncmin.c -o uncmin.o
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dchdc.f -o dchdc.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dpbfa.f -o dpbfa.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dpbsl.f -o dpbsl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dpoco.f -o dpoco.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dpodi.f -o dpodi.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dpofa.f -o dpofa.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dposl.f -o dposl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dqrdc.f -o dqrdc.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dqrdc2.f -o dqrdc2.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dqrls.f -o dqrls.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dqrsl.f -o dqrsl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dqrutl.f -o dqrutl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dsvdc.f -o dsvdc.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dtrco.f -o dtrco.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dtrsl.f -o dtrsl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o  
ranlib libappl.a
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/appl'
#@make install-Linpack
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/appl'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/nmath'
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mlutils.c -o mlutils.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c d1mach.c -o d1mach.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c i1mach.c -o i1mach.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fmax2.c -o fmax2.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fmin2.c -o fmin2.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fprec.c -o fprec.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fround.c -o fround.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ftrunc.c -o ftrunc.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sign.c -o sign.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fsign.c -o fsign.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c imax2.c -o imax2.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c imin2.c -o imin2.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chebyshev.c -o chebyshev.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c log1p.c -o log1p.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lgammacor.c -o lgammacor.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gammalims.c -o gammalims.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c stirlerr.c -o stirlerr.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bd0.c -o bd0.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gamma.c -o gamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lgamma.c -o lgamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gamma_cody.c -o gamma_cody.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c beta.c -o beta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lbeta.c -o lbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c polygamma.c -o polygamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cospi.c -o cospi.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bessel_i.c -o bessel_i.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bessel_j.c -o bessel_j.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bessel_k.c -o bessel_k.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bessel_y.c -o bessel_y.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c choose.c -o choose.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c snorm.c -o snorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sexp.c -o sexp.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dgamma.c -o dgamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pgamma.c -o pgamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qgamma.c -o qgamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rgamma.c -o rgamma.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dbeta.c -o dbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pbeta.c -o pbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qbeta.c -o qbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rbeta.c -o rbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dunif.c -o dunif.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c punif.c -o punif.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qunif.c -o qunif.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c runif.c -o runif.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dnorm.c -o dnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pnorm.c -o pnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qnorm.c -o qnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rnorm.c -o rnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dlnorm.c -o dlnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plnorm.c -o plnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qlnorm.c -o qlnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rlnorm.c -o rlnorm.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c df.c -o df.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pf.c -o pf.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qf.c -o qf.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rf.c -o rf.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dnf.c -o dnf.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dt.c -o dt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pt.c -o pt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qt.c -o qt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rt.c -o rt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dnt.c -o dnt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dchisq.c -o dchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pchisq.c -o pchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qchisq.c -o qchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rchisq.c -o rchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rnchisq.c -o rnchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dbinom.c -o dbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pbinom.c -o pbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qbinom.c -o qbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rbinom.c -o rbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rmultinom.c -o rmultinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dcauchy.c -o dcauchy.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pcauchy.c -o pcauchy.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qcauchy.c -o qcauchy.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rcauchy.c -o rcauchy.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dexp.c -o dexp.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pexp.c -o pexp.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qexp.c -o qexp.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rexp.c -o rexp.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dgeom.c -o dgeom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pgeom.c -o pgeom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qgeom.c -o qgeom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rgeom.c -o rgeom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dhyper.c -o dhyper.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c phyper.c -o phyper.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qhyper.c -o qhyper.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rhyper.c -o rhyper.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dnbinom.c -o dnbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pnbinom.c -o pnbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qnbinom.c -o qnbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rnbinom.c -o rnbinom.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dpois.c -o dpois.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ppois.c -o ppois.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qpois.c -o qpois.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpois.c -o rpois.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dweibull.c -o dweibull.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pweibull.c -o pweibull.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qweibull.c -o qweibull.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rweibull.c -o rweibull.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dlogis.c -o dlogis.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plogis.c -o plogis.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qlogis.c -o qlogis.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rlogis.c -o rlogis.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dnchisq.c -o dnchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pnchisq.c -o pnchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qnchisq.c -o qnchisq.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dnbeta.c -o dnbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pnbeta.c -o pnbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qnbeta.c -o qnbeta.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pnf.c -o pnf.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pnt.c -o pnt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qnf.c -o qnf.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qnt.c -o qnt.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ptukey.c -o ptukey.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qtukey.c -o qtukey.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c toms708.c -o toms708.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c wilcox.c -o wilcox.o
gcc -m64 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c signrank.c -o signrank.o
ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/nmath'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/nmath'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/unix'
config.status: creating src/unix/Makefile
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/unix'
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Rembedded.c -o Rembedded.o
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dynload.c -o dynload.o
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c system.c -o system.o
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sys-unix.c -o sys-unix.o
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sys-std.c -o sys-std.o
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c X11.c -o X11.o
ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/unix'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/unix'
gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -DR_HOME='"/builddir/build/BUILD/R-4.1.0"' \
  -o Rscript ./Rscript.c
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/unix'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/unix'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/main'
config.status: creating src/main/Makefile
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making altclasses.d from altclasses.c
making altrep.d from altrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making patterns.d from patterns.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/main'
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c CommandLineArgs.c -o CommandLineArgs.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Rdynload.c -o Rdynload.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Renviron.c -o Renviron.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c RNG.c -o RNG.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agrep.c -o agrep.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c altclasses.c -o altclasses.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c altrep.c -o altrep.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c apply.c -o apply.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c arithmetic.c -o arithmetic.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c array.c -o array.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c attrib.c -o attrib.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bind.c -o bind.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c builtin.c -o builtin.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c character.c -o character.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coerce.c -o coerce.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c colors.c -o colors.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c complex.c -o complex.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c connections.c -o connections.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c context.c -o context.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cum.c -o cum.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dcf.c -o dcf.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c datetime.c -o datetime.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c debug.c -o debug.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c deparse.c -o deparse.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devices.c -o devices.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dotcode.c -o dotcode.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dounzip.c -o dounzip.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dstruct.c -o dstruct.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c duplicate.c -o duplicate.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c edit.c -o edit.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c engine.c -o engine.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c envir.c -o envir.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c errors.c -o errors.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c eval.c -o eval.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c format.c -o format.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gevents.c -o gevents.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gram.c -o gram.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gram-ex.c -o gram-ex.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c graphics.c -o graphics.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c grep.c -o grep.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c identical.c -o identical.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c inlined.c -o inlined.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c inspect.c -o inspect.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c internet.c -o internet.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c iosupport.c -o iosupport.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lapack.c -o lapack.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c list.c -o list.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c localecharset.c -o localecharset.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c logic.c -o logic.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c main.c -o main.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mapply.c -o mapply.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match.c -o match.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c memory.c -o memory.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c names.c -o names.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c objects.c -o objects.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c options.c -o options.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c paste.c -o paste.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c patterns.c -o patterns.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c platform.c -o platform.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plot.c -o plot.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plot3d.c -o plot3d.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plotmath.c -o plotmath.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c print.c -o print.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c printarray.c -o printarray.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c printvector.c -o printvector.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c printutils.c -o printutils.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qsort.c -o qsort.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c radixsort.c -o radixsort.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c random.c -o random.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c raw.c -o raw.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c registration.c -o registration.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c relop.c -o relop.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rlocale.c -o rlocale.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c saveload.c -o saveload.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c scan.c -o scan.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c seq.c -o seq.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c serialize.c -o serialize.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sort.c -o sort.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c source.c -o source.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c split.c -o split.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sprintf.c -o sprintf.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c startup.c -o startup.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c subassign.c -o subassign.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c subscript.c -o subscript.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c subset.c -o subset.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c summary.c -o summary.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sysutils.c -o sysutils.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c times.c -o times.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c unique.c -o unique.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c util.c -o util.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c version.c -o version.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c g_alab_her.c -o g_alab_her.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c g_cntrlify.c -o g_cntrlify.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c g_fontdb.c -o g_fontdb.o
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c g_her_glyph.c -o g_her_glyph.o
gfortran -m64 -fno-optimize-sibling-calls -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c xxxpr.f -o xxxpr.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -shared -fopenmp -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld   -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o patterns.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o`  ../extra/xdr/libxdr.a   -lopenblas -lgfortran -lm -lquadmath   -lreadline  -ltre -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/main'
mkdir -p -- /builddir/build/BUILD/R-4.1.0/bin/exec
mkdir -p -- /builddir/build/BUILD/R-4.1.0/lib
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/main'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/main'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/main'
gcc -m64  -I../../src/extra/xdr -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Rmain.c -o Rmain.o
gcc -m64 -Wl,--export-dynamic -fopenmp  -L"../../lib" -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o R.bin Rmain.o  -lR 
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/main'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/main'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/main'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/main'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/internet'
making Rhttpd.d from Rhttpd.c
making Rsock.d from Rsock.c
making internet.d from internet.c
making libcurl.d from libcurl.c
making nanoftp.d from nanoftp.c
making nanohttp.d from nanohttp.c
making sock.d from sock.c
making sockconn.d from sockconn.c
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/internet'
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c Rsock.c -o Rsock.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c internet.c -o internet.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c libcurl.c -o libcurl.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c nanoftp.c -o nanoftp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c nanohttp.c -o nanohttp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c sock.c -o sock.o
gcc -m64 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -m64 -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR  
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILD/R-4.1.0/modules
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/internet'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/internet'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/internet'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/lapack'
making Lapack.d from Lapack.c
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/lapack'
gcc -m64 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Lapack.c -o Lapack.o
gcc -m64 -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o lapack.so  Lapack.o  -lR   -lopenblas -lgfortran -lm -lquadmath
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/lapack'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/lapack'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/lapack'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/lapack'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/X11'
making devX11.d from devX11.c
making rotated.d from rotated.c
making rbitmap.d from rbitmap.c
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/modules/X11'
gcc -m64 -I/usr/include/libpng16   -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/libxml2 -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devX11.c -o devX11.o
gcc -m64 -I/usr/include/libpng16   -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/libxml2 -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rotated.c -o rotated.o
gcc -m64 -I/usr/include/libpng16   -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/libxml2 -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rbitmap.c -o rbitmap.o
gcc -m64 -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff  -ljpeg  -lpng16 -lz  -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext  -lX11 -lXt -lXmu  -lR -lm 
gcc -m64 -I/usr/include/libpng16   -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/libxml2 -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dataentry.c -o dataentry.o
gcc -m64 -shared -L"../../../lib" -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext  -lX11 -lXt -lXmu  -lR -lm 
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/X11'
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make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules/X11'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/modules'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
mkdir -p -- ../../library
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/profile'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/translations'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/translations'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/translations'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
building package 'base'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
mkdir -p -- ../../../library/base/demo
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
making pdscan.d from pdscan.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c text.c -o text.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Rmd5.c -o Rmd5.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c md5.c -o md5.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c signals.c -o signals.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c install.c -o install.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c getfmts.c -o getfmts.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c http.c -o http.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gramLatex.c -o gramLatex.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gramRd.c -o gramRd.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pdscan.c -o pdscan.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o pdscan.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
installing 'sysdata.rda'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/compiler'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/compiler'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/compiler'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tools'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mkdir -p -- ../../../library/utils/misc
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils/src'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
making utils.d from utils.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c io.c -o io.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c size.c -o size.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sock.c -o sock.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c stubs.c -o stubs.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c utils.c -o utils.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
installing 'sysdata.rda'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/utils'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
mkdir -p -- ../../../library/grDevices/R
mkdir -p -- ../../../library/grDevices/afm
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/icc
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src'
making axis_scales.d from axis_scales.c
making chull.d from chull.c
making devices.d from devices.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making clippath.d from clippath.c
making patterns.d from patterns.c
making mask.d from mask.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c axis_scales.c -o axis_scales.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chull.c -o chull.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devices.c -o devices.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c stubs.c -o stubs.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c colors.c -o colors.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c clippath.c -o clippath.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c patterns.c -o patterns.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mask.c -o mask.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devCairo.c -o devCairo.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devPicTeX.c -o devPicTeX.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devPS.c -o devPS.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c devQuartz.c -o devQuartz.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o clippath.o patterns.o mask.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src/cairo'
make[9]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src/cairo'
gcc -m64 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/libxml2 -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cairoBM.c -o cairoBM.o
gcc -m64 -shared -L"../../../../../lib" -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff  -ljpeg  -lpng16 -lz  -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo  -L"../../../../../lib" -lR -lm 
make[9]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src/cairo'
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grDevices'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics/src'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making stem.d from stem.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c base.c -o base.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c graphics.c -o graphics.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c par.c -o par.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plot.c -o plot.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c plot3d.c -o plot3d.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c stem.c -o stem.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/graphics'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
making influence.d from influence.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c kmeans.c -o kmeans.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ansari.c -o ansari.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bandwidths.c -o bandwidths.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chisqsim.c -o chisqsim.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c d2x2xk.c -o d2x2xk.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fexact.c -o fexact.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c kendall.c -o kendall.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ks.c -o ks.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c line.c -o line.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c smooth.c -o smooth.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c prho.c -o prho.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c swilk.c -o swilk.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ksmooth.c -o ksmooth.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c loessc.c -o loessc.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c monoSpl.c -o monoSpl.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c isoreg.c -o isoreg.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Srunmed.c -o Srunmed.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dblcen.c -o dblcen.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c distance.c -o distance.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c hclust-utils.c -o hclust-utils.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c nls.c -o nls.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rWishart.c -o rWishart.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c HoltWinters.c -o HoltWinters.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c PPsum.c -o PPsum.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c arima.c -o arima.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c burg.c -o burg.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c filter.c -o filter.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mAR.c -o mAR.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pacf.c -o pacf.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c starma.c -o starma.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c port.c -o port.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c family.c -o family.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sbart.c -o sbart.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c approx.c -o approx.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c loglin.c -o loglin.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lowess.c -o lowess.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c massdist.c -o massdist.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c splines.c -o splines.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lm.c -o lm.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c complete_cases.c -o complete_cases.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cov.c -o cov.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c deriv.c -o deriv.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fft.c -o fft.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fourier.c -o fourier.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c model.c -o model.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c optim.c -o optim.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c optimize.c -o optimize.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c integrate.c -o integrate.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c random.c -o random.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c distn.c -o distn.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c zeroin.c -o zeroin.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rcont.c -o rcont.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c influence.c -o influence.o
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c bsplvd.f -o bsplvd.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c bvalue.f -o bvalue.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c bvalus.f -o bvalus.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c loessf.f -o loessf.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c ppr.f -o ppr.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c qsbart.f -o qsbart.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c sgram.f -o sgram.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c sinerp.f -o sinerp.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c sslvrg.f -o sslvrg.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c stxwx.f -o stxwx.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c hclust.f -o hclust.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c kmns.f -o kmns.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c eureka.f -o eureka.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c stl.f -o stl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -msse2 -mfpmath=sse  -c portsrc.f -o portsrc.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
portsrc.f: In function 'i7do_':
portsrc.f:6663:72: warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
 6663 |          NCOMP = NCOMP + 1
      |                                                                        ^
portsrc.f:6648:72: warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
 6648 |          LIST(JCOL) = NUMORD
      |                                                                        ^
portsrc.f: In function 'dl7mst_':
portsrc.f:5521:51: warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
 5521 |       IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
      |                                                   ^
portsrc.f:5658:18: warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
 5658 |               IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
      |                  ^
portsrc.f: In function 'dg7qts_':
portsrc.f:10329:55: warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
10329 |       IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
      |                                                       ^
portsrc.f:10412:72: warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
10412 |       V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
      |                                                                        ^
portsrc.f:10324:72: warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
10324 |       LK = DMAX1(LK, PHI*W(PHIPIN))
      |                                                                        ^
portsrc.f:10466:10: warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
10466 |       IF (KA .GE. KAMIN) GO TO 340
      |          ^
portsrc.f: In function 'dd7dgb_':
portsrc.f:12243:72: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
12243 |       V(NREDUC) = NRED
      |                                                                        ^
portsrc.f:12246:72: warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
12246 |       V(DST0) = DNWTST
      |                                                                        ^
portsrc.f: In function 'dg7qsb_':
portsrc.f:2515:72: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
 2515 |       V(NREDUC) = NRED
      |                                                                        ^
portsrc.f:2514:72: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
 2514 |  60   V(DST0) = DS0
      |                                                                        ^
portsrc.f: In function 'dl7msb_':
portsrc.f:8174:72: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
 8174 |       V(NREDUC) = NRED
      |                                                                        ^
portsrc.f:8173:72: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
 8173 |  90   V(DST0) = DS0
      |                                                                        ^
portsrc.f: In function 'df7hes_':
portsrc.f:8652:72: warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
 8652 |  210  IV(FDH) = HES
      |                                                                        ^
portsrc.f: In function 'dparck_':
portsrc.f:3587:10: warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
 3587 |       IF (LIV .LT. MIV2) GO TO 300
      |          ^
portsrc.f: In function 'drn2gb_':
portsrc.f:12079:72: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
12079 |  270  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
      |                                                                        ^
portsrc.f: In function 'drn2g_':
portsrc.f:458:72: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  458 |  300  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
      |                                                                        ^
portsrc.f:366:72: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  366 |       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
      |                                                                        ^
portsrc.f:366:72: warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -m64 -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c lminfl.f -o lminfl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/datasets'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/datasets'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
making utils.d from utils.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c do_substitute_direct.c -o do_substitute_direct.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c methods_list_dispatch.c -o methods_list_dispatch.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c slot.c -o slot.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c class_support.c -o class_support.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c tests.c -o tests.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c utils.c -o utils.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/methods/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/methods/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
byte-compiling package 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/methods'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grid/src'
making clippath.d from clippath.c
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making mask.d from mask.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c clippath.c -o clippath.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gpar.c -o gpar.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c grid.c -o grid.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c just.c -o just.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c layout.c -o layout.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mask.c -o mask.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c matrix.c -o matrix.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c register.c -o register.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c state.c -o state.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c unit.c -o unit.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c util.c -o util.o
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c viewport.c -o viewport.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grid/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grid/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
byte-compiling package 'grid'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/grid'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/splines/src'
making splines.d from splines.c
gcc -m64 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c splines.c -o splines.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o splines.so splines.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/splines/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/splines/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
byte-compiling package 'splines'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/splines'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats4'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/stats4'
byte-compiling package 'stats4'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats4'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/stats4'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk/src'
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c tcltk.c -o tcltk.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c tcltk_unix.c -o tcltk_unix.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.6 -L/usr/lib64 -ltk8.6 -lX11 -lm -L../../../../lib -lR
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk/src'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk'
byte-compiling package 'tcltk'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/tcltk'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
make[5]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel/src'
making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rngstream.c -o rngstream.o
gcc -m64 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fork.c -o fork.o
gcc -m64 -shared -L../../../../lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[6]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[6]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel/src'
make[5]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel/src'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
byte-compiling package 'parallel'
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/parallel'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/base'
installing parsed NAMESPACE files
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
make[1]: Nothing to be done for 'R'.
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
you should 'make docs' now ...
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/doc'
creating doc/NEWS
creating doc/NEWS.pdf
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/doc/manual'
creating doc/manual/R-FAQ.html
creating doc/manual/version.texi
creating doc/manual/R-admin.html
creating doc/manual/R-data.html
creating doc/manual/R-exts.html
creating doc/manual/R-intro.html
creating doc/manual/R-ints.html
creating doc/manual/R-lang.html
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/doc/html'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/doc/html'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/doc/manual'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/doc'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
installing parsed Rd
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
building/updating package metadata ...
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
writing package indices
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
building all R object docs
  converting help for package 'base'
    Arithmetic                              html  
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    base-defunct                            html  
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  converting help for package 'tools'
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    Rprof                                   html  
    Rprofmem                                html  
    Rscript                                 html  
    Rtangle                                 html  
    RweaveLatex                             html  
    SHLIB                                   html  
    Sweave                                  html  
    SweaveSyntConv                          html  
    SweaveUtils                             html  
    URLencode                               html  
    View                                    html  
    adist                                   html  
    alarm                                   html  
    apropos                                 html  
    aregexec                                html  
    arrangeWindows                          html  
    askYesNo                                html  
    aspell-utils                            html  
    aspell                                  html  
    available.packages                      html  
    bibentry                                html  
    browseEnv                               html  
    browseURL                               html  
    browseVignettes                         html  
    bug.report                              html  
    capture.output                          html  
    changedFiles                            html  
    charClass                               html  
    choose.dir                              html  
    choose.files                            html  
    chooseBioCmirror                        html  
    chooseCRANmirror                        html  
    citEntry                                html  
    citation                                html  
    cite                                    html  
    clipboard                               html  
    close.socket                            html  
    combn                                   html  
    compareVersion                          html  
    contrib.url                             html  
    count.fields                            html  
    create.post                             html  
    data                                    html  
    dataentry                               html  
    debugcall                               html  
    debugger                                html  
    demo                                    html  
    download.file                           html  
    download.packages                       html  
    edit                                    html  
    edit.data.frame                         html  
    example                                 html  
    file.edit                               html  
    filetest                                html  
    findLineNum                             html  
    fix                                     html  
    flush.console                           html  
    format                                  html  
    getAnywhere                             html  
    getFromNamespace                        html  
    getParseData                            html  
    getS3method                             html  
    getWindowsHandle                        html  
    getWindowsHandles                       html  
    glob2rx                                 html  
    globalVariables                         html  
    hasName                                 html  
    head                                    html  
    help                                    html  
    help.request                            html  
    help.search                             html  
    help.start                              html  
    hsearch-utils                           html  
    install.packages                        html  
    installed.packages                      html  
    isS3method                              html  
    isS3stdGen                              html  
    localeToCharset                         html  
    ls_str                                  html  
    maintainer                              html  
    make.packages.html                      html  
    make.socket                             html  
    memory.size                             html  
    menu                                    html  
    methods                                 html  
    mirrorAdmin                             html  
    modifyList                              html  
    news                                    html  
    nsl                                     html  
    object.size                             html  
    package.skeleton                        html  
    packageDescription                      html  
    packageName                             html  
    packageStatus                           html  
    page                                    html  
    person                                  html  
    process.events                          html  
    prompt                                  html  
    promptData                              html  
    promptPackage                           html  
    rcompgen                                html  
    read.DIF                                html  
    read.fortran                            html  
    read.fwf                                html  
    read.socket                             html  
    read.table                              html  
    readRegistry                            html  
    recover                                 html  
    relist                                  html  
    remove.packages                         html  
    removeSource                            html  
    roman                                   html  
    rtags                                   html  
    savehistory                             html  
    select.list                             html  
    sessionInfo                             html  
    setRepositories                         html  
    setWindowTitle                          html  
    shortPathName                           html  
    sourceutils                             html  
    stack                                   html  
    str                                     html  
    strcapture                              html  
    summaryRprof                            html  
    tar                                     html  
    toLatex                                 html  
    txtProgressBar                          html  
    type.convert                            html  
    untar                                   html  
    unzip                                   html  
    update.packages                         html  
    url.show                                html  
    utils-defunct                           html  
    utils-deprecated                        html  
    utils-package                           html  
    vignette                                html  
    warnErrList                             html  
    winDialog                               html  
    winMenus                                html  
    winProgressBar                          html  
    winextras                               html  
    write.table                             html  
    zip                                     html  
  converting help for package 'grDevices'
    Devices                                 html  
    Hershey                                 html  
    Japanese                                html  
    Type1Font                               html  
    adjustcolor                             html  
    as.graphicsAnnot                        html  
    as.raster                               html  
    axisTicks                               html  
    boxplot.stats                           html  
    bringToTop                              html  
    cairo                                   html  
    cairoSymbolFont                         html  
    check.options                           html  
    chull                                   html  
    cm                                      html  
    col2rgb                                 html  
    colorRamp                               html  
    colors                                  html  
    contourLines                            html  
    convertColor                            html  
    densCols                                html  
    dev                                     html  
    dev.capabilities                        html  
    dev.capture                             html  
    dev.flush                               html  
    dev.interactive                         html  
    dev.size                                html  
    dev2                                    html  
    dev2bitmap                              html  
    devAskNewPage                           html  
    embedFonts                              html  
    extendrange                             html  
    getGraphicsEvent                        html  
    grDevices-package                       html  
    grSoftVersion                           html  
    gray                                    html  
    gray.colors                             html  
    hcl                                     html  
    hsv                                     html  
    make.rgb                                html  
    msgWindow                               html  
    n2mfrow                                 html  
    nclass                                  html  
    palette                                 html  
    palettes                                html  
    pdf                                     html  
    pdf.options                             html  
    pictex                                  html  
    plotmath                                html  
    postscript                              html  
    postscriptFonts                         html  
    pretty.Date                             html  
    ps.options                              html  
    quartz                                  html  
    quartzFonts                             html  
    recordGraphics                          html  
    recordplot                              html  
    rgb                                     html  
    rgb2hsv                                 html  
    trans3d                                 html  
    windows                                 html  
    windows.options                         html  
    windowsFonts                            html  
    x11                                     html  
    x11Fonts                                html  
    xfig                                    html  
    xy.coords                               html  
    xyTable                                 html  
    xyz.coords                              html  
    png                                     html  
    savePlot                                html  
  converting help for package 'graphics'
    abline                                  html  
    arrows                                  html  
    assocplot                               html  
    axTicks                                 html  
    axis.POSIXct                            html  
    axis                                    html  
    barplot                                 html  
    box                                     html  
    boxplot                                 html  
    boxplot.matrix                          html  
    bxp                                     html  
    cdplot                                  html  
    clip                                    html  
    contour                                 html  
    convertXY                               html  
    coplot                                  html  
    curve                                   html  
    dotchart                                html  
    filled.contour                          html  
    fourfoldplot                            html  
    frame                                   html  
    graphics-defunct                        html  
    graphics-package                        html  
    grid                                    html  
    hist.POSIXt                             html  
    hist                                    html  
    identify                                html  
    image                                   html  
    layout                                  html  
    legend                                  html  
    lines                                   html  
    locator                                 html  
    matplot                                 html  
    mosaicplot                              html  
    mtext                                   html  
    pairs                                   html  
    panel.smooth                            html  
    par                                     html  
    persp                                   html  
    pie                                     html  
    plot.dataframe                          html  
    plot.default                            html  
    plot.design                             html  
    plot.factor                             html  
    plot.formula                            html  
    plot.raster                             html  
    plot.table                              html  
    plot.window                             html  
    plot.xy                                 html  
    plothistogram                           html  
    points                                  html  
    polygon                                 html  
    polypath                                html  
    rasterImage                             html  
    rect                                    html  
    rug                                     html  
    screen                                  html  
    segments                                html  
    smoothScatter                           html  
    spineplot                               html  
    stars                                   html  
    stem                                    html  
    stripchart                              html  
    strwidth                                html  
    sunflowerplot                           html  
    symbols                                 html  
    text                                    html  
    title                                   html  
    units                                   html  
    xspline                                 html  
    zAxis                                   html  
  converting help for package 'stats'
    AIC                                     html  
    ARMAacf                                 html  
    ARMAtoMA                                html  
    Beta                                    html  
    Binomial                                html  
    Cauchy                                  html  
    Chisquare                               html  
    Distributions                           html  
    Exponential                             html  
    Fdist                                   html  
    GammaDist                               html  
    Geometric                               html  
    HoltWinters                             html  
    Hypergeometric                          html  
    IQR                                     html  
    KalmanLike                              html  
    Logistic                                html  
    Lognormal                               html  
    Multinom                                html  
    NLSstAsymptotic                         html  
    NLSstClosestX                           html  
    NLSstLfAsymptote                        html  
    NLSstRtAsymptote                        html  
    NegBinomial                             html  
    Normal                                  html  
    Pair                                    html  
    Poisson                                 html  
    SSD                                     html  
    SSasymp                                 html  
    SSasympOff                              html  
    SSasympOrig                             html  
    SSbiexp                                 html  
    SSfol                                   html  
    SSfpl                                   html  
    SSgompertz                              html  
    SSlogis                                 html  
    SSmicmen                                html  
    SSweibull                               html  
    SignRank                                html  
    StructTS                                html  
    TDist                                   html  
    Tukey                                   html  
    TukeyHSD                                html  
    Uniform                                 html  
    Weibull                                 html  
    Wilcoxon                                html  
    acf                                     html  
    acf2AR                                  html  
    add1                                    html  
    addmargins                              html  
    aggregate                               html  
    alias                                   html  
    anova                                   html  
    anova.glm                               html  
    anova.lm                                html  
    anova.mlm                               html  
    ansari.test                             html  
    aov                                     html  
    approxfun                               html  
    ar                                      html  
    ar.ols                                  html  
    arima                                   html  
    arima.sim                               html  
    arima0                                  html  
    as.hclust                               html  
    asOneSidedFormula                       html  
    ave                                     html  
    bandwidth                               html  
    bartlett.test                           html  
    binom.test                              html  
    biplot                                  html  
    biplot.princomp                         html  
    birthday                                html  
    box.test                                html  
    cancor                                  html  
    case.names                              html  
    checkMFClasses                          html  
    chisq.test                              html  
    cmdscale                                html  
    coef                                    html  
    complete.cases                          html  
    confint                                 html  
    constrOptim                             html  
    contrast                                html  
    contrasts                               html  
    convolve                                html  
    cophenetic                              html  
    cor                                     html  
    cor.test                                html  
    cov.wt                                  html  
    cpgram                                  html  
    cutree                                  html  
    decompose                               html  
    delete.response                         html  
    dendrapply                              html  
    dendrogram                              html  
    density                                 html  
    deriv                                   html  
    deviance                                html  
    df.residual                             html  
    diffinv                                 html  
    dist                                    html  
    dummy.coef                              html  
    ecdf                                    html  
    eff.aovlist                             html  
    effects                                 html  
    embed                                   html  
    expand.model.frame                      html  
    extractAIC                              html  
    factanal                                html  
    factor.scope                            html  
    family                                  html  
    fft                                     html  
    filter                                  html  
    fisher.test                             html  
    fitted.values                           html  
    fivenum                                 html  
    fligner.test                            html  
    formula                                 html  
    formula.nls                             html  
    friedman.test                           html  
    ftable                                  html  
    ftable.formula                          html  
    getInitial                              html  
    glm                                     html  
    glm.control                             html  
    glm.summaries                           html  
    hclust                                  html  
    heatmap                                 html  
    identify.hclust                         html  
    influence.measures                      html  
    integrate                               html  
    interaction.plot                        html  
    is.empty                                html  
    isoreg                                  html  
    kernapply                               html  
    kernel                                  html  
    kmeans                                  html  
    kruskal.test                            html  
    ks.test                                 html  
    ksmooth                                 html  
    lag                                     html  
    lag.plot                                html  
    line                                    html  
    listof                                  html  
    lm                                      html  
    lm.influence                            html  
    lm.summaries                            html  
    lmfit                                   html  
    loadings                                html  
    loess                                   html  
    loess.control                           html  
    logLik                                  html  
    loglin                                  html  
    lowess                                  html  
    ls.diag                                 html  
    ls.print                                html  
    lsfit                                   html  
    mad                                     html  
    mahalanobis                             html  
    make.link                               html  
    makepredictcall                         html  
    manova                                  html  
    mantelhaen.test                         html  
    mauchly.test                            html  
    mcnemar.test                            html  
    median                                  html  
    medpolish                               html  
    model.extract                           html  
    model.frame                             html  
    model.matrix                            html  
    model.tables                            html  
    monthplot                               html  
    mood.test                               html  
    na.action                               html  
    na.contiguous                           html  
    na.fail                                 html  
    nafns                                   html  
    naprint                                 html  
    nextn                                   html  
    nlm                                     html  
    nlminb                                  html  
    nls                                     html  
    nls.control                             html  
    nobs                                    html  
    numericDeriv                            html  
    offset                                  html  
    oneway.test                             html  
    optim                                   html  
    optimize                                html  
    order.dendrogram                        html  
    p.adjust                                html  
    pairwise.prop.test                      html  
    pairwise.t.test                         html  
    pairwise.table                          html  
    pairwise.wilcox.test                    html  
    plot.HoltWinters                        html  
    plot.acf                                html  
    plot.density                            html  
    plot.isoreg                             html  
    plot.lm                                 html  
    plot.ppr                                html  
    plot.profile.nls                        html  
    plot.spec                               html  
    plot.stepfun                            html  
    plot.ts                                 html  
    poisson.test                            html  
    poly                                    html  
    power                                   html  
    power.anova.test                        html  
    power.prop.test                         html  
    power.t.test                            html  
    pp.test                                 html  
    ppoints                                 html  
    ppr                                     html  
    prcomp                                  html  
    predict.HoltWinters                     html  
    predict                                 html  
    predict.arima                           html  
    predict.glm                             html  
    predict.lm                              html  
    predict.loess                           html  
    predict.nls                             html  
    predict.smooth.spline                   html  
    preplot                                 html  
    princomp                                html  
    print.power.htest                       html  
    print.ts                                html  
    printCoefmat                            html  
    profile                                 html  
    profile.nls                             html  
    proj                                    html  
    prop.test                               html  
    prop.trend.test                         html  
    qqnorm                                  html  
    quade.test                              html  
    quantile                                html  
    r2dtable                                html  
    rWishart                                html  
    read.ftable                             html  
    rect.hclust                             html  
    relevel                                 html  
    reorder.dendrogram                      html  
    reorder.factor                          html  
    replications                            html  
    reshape                                 html  
    residuals                               html  
    runmed                                  html  
    scatter.smooth                          html  
    screeplot                               html  
    sd                                      html  
    se.contrast                             html  
    selfStart                               html  
    setNames                                html  
    shapiro.test                            html  
    sigma                                   html  
    simulate                                html  
    smooth                                  html  
    smooth.spline                           html  
    smoothEnds                              html  
    sortedXyData                            html  
    spec.ar                                 html  
    spec.pgram                              html  
    spec.taper                              html  
    spectrum                                html  
    splinefun                               html  
    start                                   html  
    stat.anova                              html  
    stats-defunct                           html  
    stats-deprecated                        html  
    stats-package                           html  
    step                                    html  
    stepfun                                 html  
    stl                                     html  
    stlmethods                              html  
    summary.aov                             html  
    summary.glm                             html  
    summary.lm                              html  
    summary.manova                          html  
    summary.nls                             html  
    summary.princomp                        html  
    supsmu                                  html  
    symnum                                  html  
    t.test                                  html  
    termplot                                html  
    terms                                   html  
    terms.formula                           html  
    terms.object                            html  
    time                                    html  
    toeplitz                                html  
    ts-methods                              html  
    ts                                      html  
    ts.plot                                 html  
    ts.union                                html  
    tsSmooth                                html  
    tsdiag                                  html  
    tsp                                     html  
    uniroot                                 html  
    update                                  html  
    update.formula                          html  
    var.test                                html  
    varimax                                 html  
    vcov                                    html  
    weighted.mean                           html  
    weighted.residuals                      html  
    weights                                 html  
    wilcox.test                             html  
    window                                  html  
    xtabs                                   html  
    zC                                      html  
  converting help for package 'datasets'
    AirPassengers                           html  
    BJsales                                 html  
    BOD                                     html  
    ChickWeight                             html  
    DNase                                   html  
    EuStockMarkets                          html  
    Formaldehyde                            html  
    HairEyeColor                            html  
    Harman23.cor                            html  
    Harman74.cor                            html  
    Indometh                                html  
    InsectSprays                            html  
    JohnsonJohnson                          html  
    LakeHuron                               html  
    LifeCycleSavings                        html  
    Loblolly                                html  
    Nile                                    html  
    Orange                                  html  
    OrchardSprays                           html  
    PlantGrowth                             html  
    Puromycin                               html  
    Theoph                                  html  
    Titanic                                 html  
    ToothGrowth                             html  
    UCBAdmissions                           html  
    UKDriverDeaths                          html  
    UKLungDeaths                            html  
    UKgas                                   html  
    USAccDeaths                             html  
    USArrests                               html  
    USJudgeRatings                          html  
    USPersonalExpenditure                   html  
    VADeaths                                html  
    WWWusage                                html  
    WorldPhones                             html  
    ability.cov                             html  
    airmiles                                html  
    airquality                              html  
    anscombe                                html  
    attenu                                  html  
    attitude                                html  
    austres                                 html  
    beavers                                 html  
    cars                                    html  
    chickwts                                html  
    co2                                     html  
    crimtab                                 html  
    datasets-package                        html  
    discoveries                             html  
    esoph                                   html  
    euro                                    html  
    eurodist                                html  
    faithful                                html  
    freeny                                  html  
    infert                                  html  
    iris                                    html  
    islands                                 html  
    lh                                      html  
    longley                                 html  
    lynx                                    html  
    morley                                  html  
    mtcars                                  html  
    nhtemp                                  html  
    nottem                                  html  
    npk                                     html  
    occupationalStatus                      html  
    precip                                  html  
    presidents                              html  
    pressure                                html  
    quakes                                  html  
    randu                                   html  
    rivers                                  html  
    rock                                    html  
    sleep                                   html  
    stackloss                               html  
    state                                   html  
    sunspot.month                           html  
    sunspot.year                            html  
    sunspots                                html  
    swiss                                   html  
    treering                                html  
    trees                                   html  
    uspop                                   html  
    volcano                                 html  
    warpbreaks                              html  
    women                                   html  
    zCO2                                    html  
  converting help for package 'methods'
    BasicClasses                            html  
    Classes                                 html  
    Classes_Details                         html  
    Documentation                           html  
    EmptyMethodsList-class                  html  
    EnvironmentClass                        html  
    GenericFunctions                        html  
    Introduction                            html  
    LanguageClasses                         html  
    LinearMethodsList-class                 html  
    MethodDefinition-class                  html  
    MethodSupport                           html  
    MethodWithNext-class                    html  
    Methods                                 html  
    MethodsList-class                       html  
    MethodsList                             html  
    Methods_Details                         html  
    Methods_for_Nongenerics                 html  
    Methods_for_S3                          html  
    NextMethod                              html  
    ObjectsWithPackage-class                html  
    RClassUtils                             html  
    RMethodUtils                            html  
    S3Part                                  html  
    S4groupGeneric                          html  
    SClassExtension-class                   html  
    StructureClasses                        html  
    TraceClasses                            html  
    as                                      html  
    callGeneric                             html  
    canCoerce                               html  
    cbind2                                  html  
    className                               html  
    classRepresentation-class               html  
    classesToAM                             html  
    dotsMethods                             html  
    evalSource                              html  
    findClass                               html  
    findMethods                             html  
    fixPrevious                             html  
    genericFunction-class                   html  
    getClass                                html  
    getMethod                               html  
    getPackageName                          html  
    hasArg                                  html  
    implicitGeneric                         html  
    inheritedSlotNames                      html  
    initialize-methods                      html  
    is                                      html  
    isSealedMethod                          html  
    languageEl                              html  
    localRefClass                           html  
    method.skeleton                         html  
    methodUtilities                         html  
    methods-defunct                         html  
    methods-deprecated                      html  
    methods-package                         html  
    new                                     html  
    nonStructure-class                      html  
    promptClass                             html  
    promptMethods                           html  
    refClass                                html  
    removeMethod                            html  
    representation                          html  
    selectSuperClasses                      html  
    setAs                                   html  
    setClass                                html  
    setClassUnion                           html  
    setGeneric                              html  
    setGroupGeneric                         html  
    setIs                                   html  
    setLoadActions                          html  
    setMethod                               html  
    setOldClass                             html  
    setSClass                               html  
    show                                    html  
    showMethods                             html  
    signature-class                         html  
    slot                                    html  
    stdRefClass                             html  
    substituteDirect                        html  
    testInheritedMethods                    html  
    validObject                             html  
    zBasicFunsList                          html  
  converting help for package 'grid'
    Grid                                    html  
    absolute.size                           html  
    arrow                                   html  
    calcStringMetric                        html  
    current.viewport                        html  
    dataViewport                            html  
    depth                                   html  
    deviceLoc                               html  
    drawDetails                             html  
    editDetails                             html  
    editViewport                            html  
    explode                                 html  
    gEdit                                   html  
    gPath                                   html  
    getNames                                html  
    gpar                                    html  
    grid-defunct                            html  
    grid-internal                           html  
    grid-package                            html  
    grid.DLapply                            html  
    grid.add                                html  
    grid.bezier                             html  
    grid.cap                                html  
    grid.circle                             html  
    grid.clip                               html  
    grid.convert                            html  
    grid.copy                               html  
    grid.curve                              html  
    grid.delay                              html  
    grid.display.list                       html  
    grid.draw                               html  
    grid.edit                               html  
    grid.force                              html  
    grid.frame                              html  
    grid.function                           html  
    grid.get                                html  
    grid.grab                               html  
    grid.grep                               html  
    grid.grill                              html  
    grid.grob                               html  
    grid.layout                             html  
    grid.lines                              html  
    grid.locator                            html  
    grid.ls                                 html  
    grid.move.to                            html  
    grid.newpage                            html  
    grid.null                               html  
    grid.pack                               html  
    grid.path                               html  
    grid.place                              html  
    grid.plot.and.legend                    html  
    grid.points                             html  
    grid.polygon                            html  
    grid.pretty                             html  
    grid.raster                             html  
    grid.record                             html  
    grid.rect                               html  
    grid.refresh                            html  
    grid.remove                             html  
    grid.reorder                            html  
    grid.roundrect                          html  
    grid.segments                           html  
    grid.set                                html  
    grid.show.layout                        html  
    grid.show.viewport                      html  
    grid.text                               html  
    grid.xaxis                              html  
    grid.xspline                            html  
    grid.yaxis                              html  
    grobCoords                              html  
    grobName                                html  
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  converting help for package 'splines'
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  converting help for package 'stats4'
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  converting help for package 'tcltk'
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  converting help for package 'compiler'
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  converting help for package 'parallel'
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make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/Recommended'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpS5VUZd/R.INSTALL3660492d1ad82d/MASS/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c MASS.c -o MASS.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lqs.c -o lqs.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o MASS.so MASS.o lqs.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpS5VUZd/R.INSTALL3660492d1ad82d/MASS/src'
installing to /builddir/build/BUILD/R-4.1.0/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MASS'
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** building package indices
** testing if installed package can be loaded
* DONE (MASS)
Making 'packages.html' ... done
begin installing recommended package lattice
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpzEXDEg/R.INSTALL36607b38439d12/lattice/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c threeDplot.c -o threeDplot.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o lattice.so init.o threeDplot.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpzEXDEg/R.INSTALL36607b38439d12/lattice/src'
installing to /builddir/build/BUILD/R-4.1.0/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lattice'
    finding HTML links ... done
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** building package indices
** testing if installed package can be loaded
* DONE (lattice)
Making 'packages.html' ... done
begin installing recommended package Matrix
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c CHMfactor.c -o CHMfactor.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Csparse.c -o Csparse.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c TMatrix_as.c -o TMatrix_as.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Tsparse.c -o Tsparse.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Mutils.c -o Mutils.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chm_common.c -o chm_common.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1409:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
 1409 |     csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
      |                  ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cs_utils.c -o cs_utils.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dense.c -o dense.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dgCMatrix.c -o dgCMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dgTMatrix.c -o dgTMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dgeMatrix.c -o dgeMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dpoMatrix.c -o dpoMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dppMatrix.c -o dppMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dsCMatrix.c -o dsCMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dsyMatrix.c -o dsyMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dspMatrix.c -o dspMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dtCMatrix.c -o dtCMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dtTMatrix.c -o dtTMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dtrMatrix.c -o dtrMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dtpMatrix.c -o dtpMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c factorizations.c -o factorizations.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ldense.c -o ldense.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lgCMatrix.c -o lgCMatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sparseQR.c -o sparseQR.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c abIndex.c -o abIndex.o
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[5]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD/Lib'
make[5]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD'
( cd Source ; make clean )
make[5]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD/Source'
make[5]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD/Source'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD'
( cd Source ; make clean )
make[5]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD/Source'
make[5]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD/Source'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/SuiteSparse_config'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/SuiteSparse_config'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD'
( cd Lib ; make -f "/builddir/build/BUILD/R-4.1.0/etc/Makeconf" -f Makefile )
make[5]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD/Lib'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:113:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   37 |     double *Lx, *Lz ;
      |                  ^~
In file included from ../Core/cholmod_change_factor.c:115:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   37 |     double *Lx, *Lz ;
      |                  ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:262:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
  262 |     Int nsuper, xsize, ssize ;
      |                 ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:677:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
  677 |     Int *Lp, *Li, *Lnz ;
      |               ^~
../Core/cholmod_change_factor.c:677:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
  677 |     Int *Lp, *Li, *Lnz ;
      |          ^~
../Core/cholmod_change_factor.c:676:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
  676 |     double *Lx, *Lz ;
      |                  ^~
../Core/cholmod_change_factor.c:676:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
  676 |     double *Lx, *Lz ;
      |             ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:824:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  824 |     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
      |         ^
../Core/cholmod_change_factor.c:823:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
  823 |     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
      |                     ^~~
../Core/cholmod_change_factor.c:823:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
  823 |     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
      |          ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:275:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
  275 |     Int nrow, ncol, up, lo, values, diag, astype ;
      |                         ^~
../Core/cholmod_copy.c:275:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
  275 |     Int nrow, ncol, up, lo, values, diag, astype ;
      |                     ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:45:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                            ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                       ^~
../Core/t_cholmod_dense.c:27:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |             ^~
In file included from ../Core/cholmod_dense.c:47:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                            ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                            ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                            ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                  ^~
In file included from ../Core/cholmod_dense.c:49:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                            ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                            ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                            ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                  ^~
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:300:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
  300 |     Int i, n, nz ;
      |               ^~
../Core/cholmod_dense.c:299:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  299 |     double *Xx, *Xz ;
      |                  ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_memory.c -o cholmod_memory.o
../Core/cholmod_memory.c: In function 'cholmod_malloc':
../Core/cholmod_memory.c:121:12: warning: unused variable 's' [-Wunused-variable]
  121 |     size_t s ;
      |            ^
../Core/cholmod_memory.c: In function 'cholmod_realloc':
../Core/cholmod_memory.c:311:12: warning: unused variable 's' [-Wunused-variable]
  311 |     size_t s ;
      |            ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:485:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  485 |     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
      |                                   ^~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:121:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                       ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c:42:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |             ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                       ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c:139:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |             ^~
In file included from ../Core/cholmod_transpose.c:123:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
In file included from ../Core/cholmod_transpose.c:125:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
In file included from ../Core/cholmod_transpose.c:130:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:105:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                            ^~
../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                       ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                  ^~
../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |             ^~
In file included from ../Core/cholmod_triplet.c:107:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                            ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                  ^~
In file included from ../Core/cholmod_triplet.c:109:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                            ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                  ^~
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
  342 |     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
      |                                            ^~
../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
  341 |     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
      |                    ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
  204 |     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
      |                                                             ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
  950 |     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
      |                                     ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1497:9: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
 1497 |         ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
      |         ^~~
../Check/cholmod_check.c:1495:16: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
 1495 |         count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
      |                ^~~~~~~
../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
 1494 |     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
      |                                      ^~~~~~~~
../Check/cholmod_check.c: In function 'check_factor.constprop.0':
../Check/cholmod_check.c:1496:62: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1496 |         jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
      |                                                              ^~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
  366 |     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
      |                                 ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
  419 |     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
      |                                                                     ^~~~
../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
  416 |     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
      |                                             ^~~~~~~
../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
  416 |     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
      |                                   ^~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  111 |     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
      |                                     ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:161:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:163:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:165:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:169:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:171:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:173:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:63:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   61 |     double *Lx, *Yx, *Yz ;
      |                       ^~
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   61 |     double *Lx, *Yx, *Yz ;
      |                       ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
  334 |     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
      |             ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:44:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   52 |     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
      |                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                               ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                      ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                            ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                  ^~
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   52 |     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
      |                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                               ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                      ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                            ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                  ^~
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   52 |     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
      |                 ^~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask2':
../Modify/cholmod_updown.c:433:40: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  433 |         *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
      |                                        ^~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:82:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
      | 
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q )  \
      | 
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  756 | #pragma omp parallel for private ( j, i, px, q )                \
      | 
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
  116 |         tail, nscol_new = 0;
      |         ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
  113 |         pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
      |         ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
  111 |         *Previous;
      |          ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                                 ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                            ^~
In file included from ../Supernodal/cholmod_super_numeric.c:84:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
      | 
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q )  \
      | 
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  756 | #pragma omp parallel for private ( j, i, px, q )                \
      | 
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
  116 |         tail, nscol_new = 0;
      |         ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
  113 |         pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
      |         ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
  111 |         *Previous;
      |          ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                                 ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                            ^~
In file included from ../Supernodal/cholmod_super_numeric.c:86:
../Supernodal/t_cholmod_super_numeric.c: In function 'z_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
      | 
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q )  \
      | 
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  756 | #pragma omp parallel for private ( j, i, px, q )                \
      | 
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
  116 |         tail, nscol_new = 0;
      |         ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
  113 |         pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
      |         ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
  111 |         *Previous;
      |          ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:26:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   30 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  238 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   30 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  238 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:562:21: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
  562 |                 Int totsize ;
      |                     ^~~~~~~
../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable]
  185 |     double max_fraction;
      |            ^~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable]
  184 |     const char* env_max_fraction;
      |                 ^~~~~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable]
  183 |     size_t max_bytes;
      |            ^~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable]
  182 |     const char* env_max_bytes;
      |                 ^~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable]
  181 |     const char* env_use_gpu;
      |                 ^~~~~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
../Core/cholmod_add.c:34:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
   34 |     double alpha [2],       /* scale factor for A */
      |     ~~~~~~~^~~~~~~~~
In file included from ../Core/cholmod_add.c:27:
../Include/cholmod_core.h:1582:68: note: previously declared as 'double *'
 1582 | cholmod_sparse *cholmod_l_add (cholmod_sparse *, cholmod_sparse *, double *,
      |                                                                    ^~~~~~~~
../Core/cholmod_add.c:35:12: warning: argument 4 of type 'double[2]' with mismatched bound [-Warray-parameter=]
   35 |     double beta [2],        /* scale factor for B */
      |     ~~~~~~~^~~~~~~~
In file included from ../Core/cholmod_add.c:27:
../Include/cholmod_core.h:1583:5: note: previously declared as 'double *'
 1583 |     double *, int, int, cholmod_common *) ;
      |     ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:113:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   37 |     double *Lx, *Lz ;
      |                  ^~
In file included from ../Core/cholmod_change_factor.c:115:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   37 |     double *Lx, *Lz ;
      |                  ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:262:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
  262 |     Int nsuper, xsize, ssize ;
      |                 ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:677:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
  677 |     Int *Lp, *Li, *Lnz ;
      |               ^~
../Core/cholmod_change_factor.c:677:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
  677 |     Int *Lp, *Li, *Lnz ;
      |          ^~
../Core/cholmod_change_factor.c:676:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
  676 |     double *Lx, *Lz ;
      |                  ^~
../Core/cholmod_change_factor.c:676:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
  676 |     double *Lx, *Lz ;
      |             ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:824:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  824 |     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
      |         ^
../Core/cholmod_change_factor.c:823:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
  823 |     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
      |                     ^~~
../Core/cholmod_change_factor.c:823:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
  823 |     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
      |          ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:275:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
  275 |     Int nrow, ncol, up, lo, values, diag, astype ;
      |                         ^~
../Core/cholmod_copy.c:275:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
  275 |     Int nrow, ncol, up, lo, values, diag, astype ;
      |                     ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:45:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                            ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                       ^~
../Core/t_cholmod_dense.c:27:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |             ^~
In file included from ../Core/cholmod_dense.c:47:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                            ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                            ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                            ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                  ^~
In file included from ../Core/cholmod_dense.c:49:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                            ^~
../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   27 |     double *Ax, *Xx, *Az, *Xz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                            ^~
../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  133 |     double *Xx, *Cx, *Xz, *Cz ;
      |                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                            ^~
../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  226 |     double *Xx, *Xz, *Yx, *Yz ;
      |                  ^~
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:300:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
  300 |     Int i, n, nz ;
      |               ^~
../Core/cholmod_dense.c:299:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
  299 |     double *Xx, *Xz ;
      |                  ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
../Core/cholmod_memory.c: In function 'cholmod_l_malloc':
../Core/cholmod_memory.c:121:12: warning: unused variable 's' [-Wunused-variable]
  121 |     size_t s ;
      |            ^
../Core/cholmod_memory.c: In function 'cholmod_l_realloc':
../Core/cholmod_memory.c:311:12: warning: unused variable 's' [-Wunused-variable]
  311 |     size_t s ;
      |            ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse':
../Core/cholmod_sparse.c:485:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  485 |     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
      |                                   ^~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:121:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                       ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c:42:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |             ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                       ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c:139:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |             ^~
In file included from ../Core/cholmod_transpose.c:123:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
In file included from ../Core/cholmod_transpose.c:125:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   42 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                            ^~
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  139 |     double *Ax, *Az, *Fx, *Fz ;
      |                  ^~
In file included from ../Core/cholmod_transpose.c:130:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   44 |     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
      |                     ^~~~
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                               ^~~
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
   43 |     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
      |                          ^~
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
  140 |     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
      |                          ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:105:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                            ^~
../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                       ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                  ^~
../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |             ^~
In file included from ../Core/cholmod_triplet.c:107:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                            ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                  ^~
In file included from ../Core/cholmod_triplet.c:109:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                            ^~
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
   28 |     double *Rx, *Rz, *Tx, *Tz ;
      |                  ^~
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
  342 |     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
      |                                            ^~
../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
  341 |     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
      |                    ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
  204 |     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
      |                                                             ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
  950 |     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
      |                                     ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1497:9: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
 1497 |         ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
      |         ^~~
../Check/cholmod_check.c:1495:16: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
 1495 |         count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
      |                ^~~~~~~
../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
 1494 |     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
      |                                      ^~~~~~~~
../Check/cholmod_check.c: In function 'check_factor.constprop.0':
../Check/cholmod_check.c:1496:62: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1496 |         jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
      |                                                              ^~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c: In function 'cholmod_l_write_sparse':
../Check/cholmod_write.c:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
  366 |     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
      |                                 ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2':
../Cholesky/cholmod_analyze.c:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
  419 |     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
      |                                                                     ^~~~
../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
  416 |     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
      |                                             ^~~~~~~
../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
  416 |     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
      |                                   ^~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c:101:12: warning: argument 2 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  101 |     double beta [2],    /* factorize beta*I+A or beta*I+A'*A */
      |     ~~~~~~~^~~~~~~~
In file included from ../Cholesky/cholmod_factorize.c:58:
../Include/cholmod_cholesky.h:168:46: note: previously declared as 'double *'
  168 | int cholmod_l_factorize_p (cholmod_sparse *, double *, SuiteSparse_long *,
      |                                              ^~~~~~~~
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  111 |     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
      |                                     ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:161:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:163:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:165:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:169:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:171:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                                ^~
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                                      ^~
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                            ^~
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   46 |     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
      |                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:173:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
   50 |         use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
      |                                                     ^~~~~
../Cholesky/cholmod_rowfac.c: At top level:
../Cholesky/cholmod_rowfac.c:577:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  577 |     double beta [2],    /* factorize beta*I+A or beta*I+AA' */
      |     ~~~~~~~^~~~~~~~
In file included from ../Cholesky/cholmod_rowfac.c:103:
../Include/cholmod_cholesky.h:387:59: note: previously declared as 'double *'
  387 | int cholmod_l_rowfac (cholmod_sparse *, cholmod_sparse *, double *, size_t,
      |                                                           ^~~~~~~~
../Cholesky/cholmod_rowfac.c:602:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  602 |     double beta [2],    /* factorize beta*I+A or beta*I+AA' */
      |     ~~~~~~~^~~~~~~~
In file included from ../Cholesky/cholmod_rowfac.c:103:
../Include/cholmod_cholesky.h:413:64: note: previously declared as 'double *'
  413 | int cholmod_l_rowfac_mask (cholmod_sparse *, cholmod_sparse *, double *, size_t,
      |                                                                ^~~~~~~~
../Cholesky/cholmod_rowfac.c:629:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  629 |     double beta [2],    /* factorize beta*I+A or beta*I+AA' */
      |     ~~~~~~~^~~~~~~~
In file included from ../Cholesky/cholmod_rowfac.c:103:
../Include/cholmod_cholesky.h:434:65: note: previously declared as 'double *'
  434 | int cholmod_l_rowfac_mask2 (cholmod_sparse *, cholmod_sparse *, double *,
      |                                                                 ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:63:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   61 |     double *Lx, *Yx, *Yz ;
      |                       ^~
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   61 |     double *Lx, *Yx, *Yz ;
      |                       ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
  334 |     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
      |             ^~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:44:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   52 |     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
      |                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                               ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                      ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                            ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                  ^~
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   52 |     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
      |                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                               ^~
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                                      ^~
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                            ^~
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
   49 |     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
      |                  ^~
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
   52 |     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
      |                 ^~~~
../MatrixOps/cholmod_sdmult.c: At top level:
../MatrixOps/cholmod_sdmult.c:59:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
   59 |     double alpha [2],   /* scale factor for A */
      |     ~~~~~~~^~~~~~~~~
In file included from ../MatrixOps/cholmod_sdmult.c:36:
../Include/cholmod_matrixops.h:143:46: note: previously declared as 'double *'
  143 | int cholmod_l_sdmult (cholmod_sparse *, int, double *, double *,
      |                                              ^~~~~~~~
../MatrixOps/cholmod_sdmult.c:60:12: warning: argument 4 of type 'double[2]' with mismatched bound [-Warray-parameter=]
   60 |     double beta [2],    /* scale factor for Y */
      |     ~~~~~~~^~~~~~~~
In file included from ../MatrixOps/cholmod_sdmult.c:36:
../Include/cholmod_matrixops.h:143:56: note: previously declared as 'double *'
  143 | int cholmod_l_sdmult (cholmod_sparse *, int, double *, double *,
      |                                                        ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
../Modify/cholmod_rowadd.c:72:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
   72 |     double bk [2],      /* kth entry of the right-hand-side b */
      |     ~~~~~~~^~~~~~
In file included from ../Modify/cholmod_rowadd.c:24:
../Include/cholmod_modify.h:215:55: note: previously declared as 'double *'
  215 | int cholmod_l_rowadd_solve (size_t, cholmod_sparse *, double *,
      |                                                       ^~~~~~~~
../Modify/cholmod_rowadd.c:116:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  116 |     double bk [2],      /* kth entry of the right hand side, b */
      |     ~~~~~~~^~~~~~
In file included from ../Modify/cholmod_rowadd.c:24:
../Include/cholmod_modify.h:241:54: note: previously declared as 'double *'
  241 | int cholmod_l_rowadd_mark (size_t, cholmod_sparse *, double *,
      |                                                      ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
../Modify/cholmod_rowdel.c:72:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
   72 |     double yk [2],      /* kth entry in the solution to A*y=b */
      |     ~~~~~~~^~~~~~
In file included from ../Modify/cholmod_rowdel.c:25:
../Include/cholmod_modify.h:294:55: note: previously declared as 'double *'
  294 | int cholmod_l_rowdel_solve (size_t, cholmod_sparse *, double *,
      |                                                       ^~~~~~~~
../Modify/cholmod_rowdel.c:104:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  104 |     double yk [2],      /* kth entry in the solution to A*y=b */
      |     ~~~~~~~^~~~~~
In file included from ../Modify/cholmod_rowdel.c:25:
../Include/cholmod_modify.h:320:54: note: previously declared as 'double *'
  320 | int cholmod_l_rowdel_mark (size_t, cholmod_sparse *, double *,
      |                                                      ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask2':
../Modify/cholmod_updown.c:433:40: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  433 |         *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
      |                                        ^~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:82:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
      | 
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q )  \
      | 
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  756 | #pragma omp parallel for private ( j, i, px, q )                \
      | 
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
  116 |         tail, nscol_new = 0;
      |         ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
  113 |         pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
      |         ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
  111 |         *Previous;
      |          ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                                 ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                            ^~
In file included from ../Supernodal/cholmod_super_numeric.c:84:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
      | 
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q )  \
      | 
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  756 | #pragma omp parallel for private ( j, i, px, q )                \
      | 
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
  116 |         tail, nscol_new = 0;
      |         ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
  113 |         pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
      |         ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
  111 |         *Previous;
      |          ^~~~~~~~
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                                 ^~
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
  108 |     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
      |                            ^~
In file included from ../Supernodal/cholmod_super_numeric.c:86:
../Supernodal/t_cholmod_super_numeric.c: In function 'z_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \
      | 
../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q )  \
      | 
../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS)   \
      | 
../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  756 | #pragma omp parallel for private ( j, i, px, q )                \
      | 
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
  116 |         tail, nscol_new = 0;
      |         ^~~~
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
  113 |         pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
      |         ^~
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
  111 |         *Previous;
      |          ^~~~~~~~
../Supernodal/cholmod_super_numeric.c: At top level:
../Supernodal/cholmod_super_numeric.c:102:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=]
  102 |     double beta [2],    /* beta*I is added to diagonal of matrix to factorize */
      |     ~~~~~~~^~~~~~~~
In file included from ../Supernodal/cholmod_super_numeric.c:60:
../Include/cholmod_supernodal.h:120:66: note: previously declared as 'double *'
  120 | int cholmod_l_super_numeric (cholmod_sparse *, cholmod_sparse *, double *,
      |                                                                  ^~~~~~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:26:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   30 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  238 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   30 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  238 |         nsrow2, n, ps2, j, i, d, nrhs ;
      |                 ^
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:562:21: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
  562 |                 Int totsize ;
      |                     ^~~~~~~
../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable]
  185 |     double max_fraction;
      |            ^~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable]
  184 |     const char* env_max_fraction;
      |                 ^~~~~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable]
  183 |     size_t max_bytes;
      |            ^~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable]
  182 |     const char* env_max_bytes;
      |                 ^~~~~~~~~~~~~
../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable]
  181 |     const char* env_use_gpu;
      |                 ^~~~~~~~~~~
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
make[5]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/CHOLMOD'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD'
( cd Source ; make -f "/builddir/build/BUILD/R-4.1.0/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD/Source'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c colamd.c -o colamd.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd.o colamd_l.o
make[5]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD/Source'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/COLAMD'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD'
( cd Source ; make -f "/builddir/build/BUILD/R-4.1.0/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD/Source'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o
make[5]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD/Source'
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/AMD'
make[4]: Entering directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/SuiteSparse_config'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG -DNTIMER  -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src/SuiteSparse_config'
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -lopenblas -lgfortran -lm -lquadmath -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpkMBu46/R.INSTALL3660ad2bb30874/Matrix/src'
installing to /builddir/build/BUILD/R-4.1.0/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix'
** help
*** installing help indices
  converting help for package 'Matrix'
    finding HTML links ... done
    BunchKaufman-methods                    html  
    CAex                                    html  
    CHMfactor-class                         html  
    Cholesky-class                          html  
    Cholesky                                html  
    CsparseMatrix-class                     html  
    Diagonal                                html  
    Hilbert                                 html  
    KNex                                    html  
    KhatriRao                               html  
    LU-class                                html  
    Matrix-class                            html  
    Matrix                                  html  
    MatrixClass                             html  
    MatrixFactorization-class               html  
    RsparseMatrix-class                     html  
    Schur-class                             html  
    Schur                                   html  
    SparseM-conv                            html  
    Subassign-methods                       html  
    TsparseMatrix-class                     html  
    USCounties                              html  
    Xtrct-methods                           html  
    abIndex-class                           html  
    abIseq                                  html  
    all-methods                             html  
    all.equal-methods                       html  
    atomicVector-class                      html  
    band                                    html  
    bandSparse                              html  
    bdiag                                   html  
    boolean-matprod                         html  
    cBind                                   html  
    chol                                    html  
    chol2inv-methods                        html  
    colSums                                 html  
    compMatrix-class                        html  
    condest                                 html  
    dMatrix-class                           html  
    ddenseMatrix-class                      html  
    ddiMatrix-class                         html  
    denseMatrix-class                       html  
    dgCMatrix-class                         html  
    dgRMatrix-class                         html  
    dgTMatrix-class                         html  
    dgeMatrix-class                         html  
    diagU2N                                 html  
    diagonalMatrix-class                    html  
REDIRECT:topic	 %/%,ddiMatrix,ddenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ddiMatrix,ldenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ddiMatrix,ndenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ldiMatrix,ddenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ldiMatrix,ldenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ldiMatrix,ndenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ddiMatrix,Matrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic	 %/%,ldiMatrix,Matrix-method -> diagonalMatrix-class.html [ FAIL ]
    dpoMatrix-class                         html  
    drop0                                   html  
    dsCMatrix-class                         html  
    dsRMatrix-class                         html  
    dsparseMatrix-class                     html  
    dsyMatrix-class                         html  
    dtCMatrix-class                         html  
    dtRMatrix-class-def                     html  
    dtpMatrix-class                         html  
    dtrMatrix-class                         html  
    expand                                  html  
    expm                                    html  
    externalFormats                         html  
    facmul                                  html  
    forceSymmetric                          html  
    formatSparseM                           html  
    generalMatrix-class                     html  
    graph2T                                 html  
    image-methods                           html  
    indMatrix-class                         html  
    index-class                             html  
    invPerm                                 html  
    is.na-methods                           html  
    is.null.DN                              html  
    isSymmetric-methods                     html  
    isTriangular                            html  
    kronecker-methods                       html  
    ldenseMatrix-class                      html  
    ldiMatrix-class                         html  
    lgeMatrix-class                         html  
    lsparseMatrix-classes                   html  
    lsyMatrix-class                         html  
    ltrMatrix-class                         html  
    lu                                      html  
    mat2triplet                             html  
    matrix-products                         html  
    nMatrix-class                           html  
    ndenseMatrix-class                      html  
    nearPD                                  html  
    ngeMatrix-class                         html  
    nnzero                                  html  
    norm                                    html  
    nsparseMatrix-classes                   html  
    nsyMatrix-class                         html  
    ntrMatrix-class                         html  
    number-class                            html  
    pMatrix-class                           html  
    printSpMatrix                           html  
    qr-methods                              html  
    rankMatrix                              html  
    rcond                                   html  
    rep2abI                                 html  
    replValue-class                         html  
    rleDiff-class                           html  
    rsparsematrix                           html  
    solve-methods                           html  
    spMatrix                                html  
    sparse.model.matrix                     html  
    sparseLU-class                          html  
    sparseMatrix-class                      html  
    sparseMatrix                            html  
    sparseQR-class                          html  
    sparseVector-class                      html  
    sparseVector                            html  
    symmetricMatrix-class                   html  
    symmpart                                html  
    triangularMatrix-class                  html  
    uniqTsparse                             html  
    unpack                                  html  
    unused-classes                          html  
    updown                                  html  
    wrld_1deg                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
begin installing recommended package nlme
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpK57bhh/R.INSTALL3662e41b67923c/nlme/src'
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c chol.f -o chol.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c corStruct.c -o corStruct.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gnls.c -o gnls.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c matrix.c -o matrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c nlOptimizer.c -o nlOptimizer.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c nlme.c -o nlme.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c nlmefit.c -o nlmefit.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pdMat.c -o pdMat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pythag.c -o pythag.o
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c rs.f -o rs.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpK57bhh/R.INSTALL3662e41b67923c/nlme/src'
installing to /builddir/build/BUILD/R-4.1.0/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nlme'
    finding HTML links ... done
    ACF                                     html  
    ACF.gls                                 html  
    ACF.lme                                 html  
    Alfalfa                                 html  
    Assay                                   html  
    BodyWeight                              html  
    Cefamandole                             html  
    Coef                                    html  
    Covariate                               html  
    Covariate.varFunc                       html  
    Dialyzer                                html  
    Dim                                     html  
    Dim.corSpatial                          html  
    Dim.corStruct                           html  
    Dim.pdMat                               html  
    Earthquake                              html  
    Extract.pdMat                           html  
    Fatigue                                 html  
    Gasoline                                html  
    Glucose                                 html  
    Glucose2                                html  
    Gun                                     html  
    IGF                                     html  
    Initialize                              html  
    Initialize.corStruct                    html  
    Initialize.glsStruct                    html  
    Initialize.lmeStruct                    html  
    Initialize.reStruct                     html  
    Initialize.varFunc                      html  
    LDEsysMat                               html  
    Machines                                html  
    MathAchSchool                           html  
    MathAchieve                             html  
    Matrix                                  html  
    Matrix.pdMat                            html  
    Matrix.reStruct                         html  
    Meat                                    html  
    Milk                                    html  
    Muscle                                  html  
    Names                                   html  
    Names.formula                           html  
    Names.pdBlocked                         html  
    Names.pdMat                             html  
    Names.reStruct                          html  
    Nitrendipene                            html  
    Oats                                    html  
    Orthodont                               html  
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    VarCorr                                 html  
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    Variogram.corRatio                      html  
    Variogram.corSpatial                    html  
    Variogram.corSpher                      html  
    Variogram.default                       html  
    Variogram.gls                           html  
    Variogram.lme                           html  
    Wafer                                   html  
    Wheat                                   html  
    Wheat2                                  html  
    allCoef                                 html  
    anova.gls                               html  
    anova.lme                               html  
    as.matrix.corStruct                     html  
    as.matrix.pdMat                         html  
    as.matrix.reStruct                      html  
    asOneFormula                            html  
    asTable                                 html  
    augPred                                 html  
    balancedGrouped                         html  
    bdf                                     html  
    coef.corStruct                          html  
    coef.gnls                               html  
    coef.lmList                             html  
    coef.lme                                html  
    coef.modelStruct                        html  
    coef.pdMat                              html  
    coef.reStruct                           html  
    coef.varFunc                            html  
    collapse                                html  
    collapse.groupedData                    html  
    compareFits                             html  
    comparePred                             html  
    corAR1                                  html  
    corARMA                                 html  
    corCAR1                                 html  
    corClasses                              html  
    corCompSymm                             html  
    corExp                                  html  
    corFactor                               html  
    corFactor.corStruct                     html  
    corGaus                                 html  
    corLin                                  html  
    corMatrix                               html  
    corMatrix.corStruct                     html  
    corMatrix.pdMat                         html  
    corMatrix.reStruct                      html  
    corNatural                              html  
    corRatio                                html  
    corSpatial                              html  
    corSpher                                html  
    corSymm                                 html  
    ergoStool                               html  
    fdHess                                  html  
    fitted.glsStruct                        html  
    fitted.gnlsStruct                       html  
    fitted.lmList                           html  
    fitted.lme                              html  
    fitted.lmeStruct                        html  
    fitted.nlmeStruct                       html  
    fixed.effects                           html  
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    formula.pdBlocked                       html  
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    formula.reStruct                        html  
    gapply                                  html  
    getCovariate                            html  
    getCovariate.corStruct                  html  
    getCovariate.data.frame                 html  
    getCovariate.varFunc                    html  
    getCovariateFormula                     html  
    getData                                 html  
    getData.gls                             html  
    getData.lmList                          html  
    getData.lme                             html  
    getGroups                               html  
    getGroups.corStruct                     html  
    getGroups.data.frame                    html  
    getGroups.gls                           html  
    getGroups.lmList                        html  
    getGroups.lme                           html  
    getGroups.varFunc                       html  
    getGroupsFormula                        html  
    getResponse                             html  
    getResponseFormula                      html  
    getVarCov                               html  
    gls-internal                            html  
    gls                                     html  
    glsControl                              html  
    glsObject                               html  
    glsStruct                               html  
    gnls                                    html  
    gnlsControl                             html  
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    groupedData                             html  
    gsummary                                html  
    intervals                               html  
    intervals.gls                           html  
    intervals.lmList                        html  
    intervals.lme                           html  
    isBalanced                              html  
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    lmList                                  html  
    lmList.groupedData                      html  
    lme                                     html  
    lme.groupedData                         html  
    lme.lmList                              html  
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    lmeObject                               html  
    lmeStruct                               html  
    logDet                                  html  
    logDet.corStruct                        html  
    logDet.pdMat                            html  
    logDet.reStruct                         html  
    logLik.corStruct                        html  
    logLik.glsStruct                        html  
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    logLik.gnlsStruct                       html  
    logLik.lmList                           html  
    logLik.lme                              html  
    logLik.lmeStruct                        html  
    logLik.reStruct                         html  
    logLik.varFunc                          html  
    model.matrix.reStruct                   html  
    needUpdate                              html  
    needUpdate.modelStruct                  html  
    nlme                                    html  
    nlme.nlsList                            html  
    nlmeControl                             html  
    nlmeObject                              html  
    nlmeStruct                              html  
    nlsList                                 html  
    nlsList.selfStart                       html  
    pairs.compareFits                       html  
    pairs.lmList                            html  
    pairs.lme                               html  
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    pdConstruct                             html  
    pdConstruct.pdBlocked                   html  
    pdDiag                                  html  
    pdFactor                                html  
    pdFactor.reStruct                       html  
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    plot.gls                                html  
    plot.intervals.lmList                   html  
    plot.lmList                             html  
    plot.lme                                html  
    plot.nffGroupedData                     html  
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    plot.nmGroupedData                      html  
    plot.ranef.lmList                       html  
    plot.ranef.lme                          html  
    pooledSD                                html  
    predict.gls                             html  
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    predict.lmList                          html  
    predict.lme                             html  
    predict.nlme                            html  
    print.summary.pdMat                     html  
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    qqnorm.gls                              html  
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    quinModel                               html  
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    ranef.lmList                            html  
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    reStruct                                html  
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    varWeights                              html  
    varWeights.glsStruct                    html  
    varWeights.lmeStruct                    html  
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done
begin installing recommended package survival
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpGqNxKL/R.INSTALL3663314a1fae4e/survival/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agexact.c -o agexact.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agfit4.c -o agfit4.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agfit5.c -o agfit5.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agmart.c -o agmart.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agmart3.c -o agmart3.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agscore2.c -o agscore2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agsurv3.c -o agsurv3.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agsurv4.c -o agsurv4.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c agsurv5.c -o agsurv5.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cdecomp.c -o cdecomp.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chinv2.c -o chinv2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chinv3.c -o chinv3.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cholesky2.c -o cholesky2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cholesky3.c -o cholesky3.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cholesky5.c -o cholesky5.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chsolve2.c -o chsolve2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chsolve3.c -o chsolve3.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c chsolve5.c -o chsolve5.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c collapse.c -o collapse.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c concordance1.c -o concordance1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c concordance3.c -o concordance3.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c cox_Rcallback.c -o cox_Rcallback.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxcount1.c -o coxcount1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxdetail.c -o coxdetail.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxexact.c -o coxexact.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxfit5.c -o coxfit5.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxfit6.c -o coxfit6.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxmart.c -o coxmart.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxmart2.c -o coxmart2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxph_wtest.c -o coxph_wtest.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxsafe.c -o coxsafe.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxscho.c -o coxscho.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxscore2.c -o coxscore2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxsurv1.c -o coxsurv1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxsurv2.c -o coxsurv2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dmatrix.c -o dmatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c doloop.c -o doloop.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c finegray.c -o finegray.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gchol.c -o gchol.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c multicheck.c -o multicheck.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c norisk.c -o norisk.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pyears1.c -o pyears1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pyears2.c -o pyears2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pyears3b.c -o pyears3b.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pystep.c -o pystep.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survConcordance.c -o survConcordance.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survdiff2.c -o survdiff2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survfit4.c -o survfit4.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survfitci.c -o survfitci.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survfitkm.c -o survfitkm.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survfitresid.c -o survfitresid.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survpenal.c -o survpenal.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survreg6.c -o survreg6.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survreg7.c -o survreg7.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survregc1.c -o survregc1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survregc2.c -o survregc2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c survsplit.c -o survsplit.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c tmerge.c -o tmerge.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c zph1.c -o zph1.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c zph2.c -o zph2.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agsurv3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o dmatrix.o doloop.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpGqNxKL/R.INSTALL3663314a1fae4e/survival/src'
installing to /builddir/build/BUILD/R-4.1.0/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'survival'
    finding HTML links ... done
    Surv                                    html  
    Surv2                                   html  
    Surv2data                               html  
    Survmethods                             html  
    aareg                                   html  
    aeqSurv                                 html  
    aggregate.survfit                       html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    blogit                                  html  
    cch                                     html  
    cgd                                     html  
    cgd0                                    html  
    cipoisson                               html  
    clogit                                  html  
    cluster                                 html  
    colon                                   html  
    concordance                             html  
    concordancefit                          html  
    cox.zph                                 html  
    coxph                                   html  
    coxph.control                           html  
    coxph.detail                            html  
    coxph.object                            html  
    coxph.wtest                             html  
    coxsurv.fit                             html  
    diabetic                                html  
    dsurvreg                                html  
    finegray                                html  
    flchain                                 html  
    frailty                                 html  
    gbsg                                    html  
    heart                                   html  
    is.ratetable                            html  
    kidney                                  html  
    levels.Surv                             html  
    lines.survfit                           html  
    logLik.coxph                            html  
    logan                                   html  
    lung                                    html  
    mgus                                    html  
    mgus2                                   html  
    model.frame.coxph                       html  
    model.matrix.coxph                      html  
    myeloid                                 html  
    nafld                                   html  
    neardate                                html  
    nsk                                     html  
    nwtco                                   html  
    ovarian                                 html  
    pbc                                     html  
    pbcseq                                  html  
    plot.aareg                              html  
    plot.cox.zph                            html  
    plot.survfit                            html  
    predict.coxph                           html  
    predict.survreg                         html  
    print.aareg                             html  
    print.summary.coxph                     html  
    print.summary.survexp                   html  
    print.summary.survfit                   html  
    print.survfit                           html  
    pseudo                                  html  
    pspline                                 html  
    pyears                                  html  
    quantile.survfit                        html  
    ratetable                               html  
    ratetableDate                           html  
    rats                                    html  
    rats2                                   html  
    reliability                             html  
    residuals.coxph                         html  
    residuals.survfit                       html  
    residuals.survreg                       html  
    retinopathy                             html  
    rhDNase                                 html  
    ridge                                   html  
    rotterdam                               html  
    royston                                 html  
    rttright                                html  
    solder                                  html  
    stanford2                               html  
    statefig                                html  
    strata                                  html  
    summary.aareg                           html  
    summary.coxph                           html  
    summary.pyears                          html  
    summary.survexp                         html  
    summary.survfit                         html  
    survSplit                               html  
    survcheck                               html  
    survdiff                                html  
    survexp                                 html  
    survexp.fit                             html  
    survexp.object                          html  
    survexp.us                              html  
    survfit                                 html  
    survfit.coxph                           html  
    survfit.formula                         html  
    survfit.matrix                          html  
    survfit.object                          html  
    survfit0                                html  
    survfitcoxph.fit                        html  
    survival-deprecated                     html  
    survival-internal                       html  
    survobrien                              html  
    survreg                                 html  
    survreg.control                         html  
    survreg.distributions                   html  
    survreg.object                          html  
    survregDtest                            html  
    tcut                                    html  
    tmerge                                  html  
    tobin                                   html  
    transplant                              html  
    udca                                    html  
    untangle.specials                       html  
    uspop2                                  html  
    vcov.coxph                              html  
    veteran                                 html  
    xtfrm.Surv                              html  
    yates                                   html  
    yates_setup                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
Making 'packages.html' ... done
begin installing recommended package boot
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'boot'
    finding HTML links ... done
    EEF.profile                             html  
    Imp.Estimates                           html  
    abc.ci                                  html  
    acme                                    html  
    aids                                    html  
    aircondit                               html  
    amis                                    html  
    aml                                     html  
    beaver                                  html  
    bigcity                                 html  
    boot-practicals                         html  
    boot                                    html  
    boot.array                              html  
    boot.ci                                 html  
    brambles                                html  
    breslow                                 html  
    calcium                                 html  
    cane                                    html  
    capability                              html  
    catsM                                   html  
    cav                                     html  
    cd4                                     html  
    cd4.nested                              html  
    censboot                                html  
    channing                                html  
    claridge                                html  
    cloth                                   html  
    co.transfer                             html  
    coal                                    html  
    control                                 html  
    corr                                    html  
    cum3                                    html  
    cv.glm                                  html  
    darwin                                  html  
    dogs                                    html  
    downs.bc                                html  
    ducks                                   html  
    empinf                                  html  
    envelope                                html  
    exp.tilt                                html  
    fir                                     html  
    freq.array                              html  
    frets                                   html  
    glm.diag                                html  
    glm.diag.plots                          html  
    gravity                                 html  
    hirose                                  html  
    imp.weights                             html  
    inv.logit                               html  
    islay                                   html  
    jack.after.boot                         html  
    k3.linear                               html  
    linear.approx                           html  
    lines.saddle.distn                      html  
    logit                                   html  
    manaus                                  html  
    melanoma                                html  
    motor                                   html  
    neuro                                   html  
    nitrofen                                html  
    nodal                                   html  
    norm.ci                                 html  
    nuclear                                 html  
    paulsen                                 html  
    plot.boot                               html  
    poisons                                 html  
    polar                                   html  
    print.boot                              html  
    print.bootci                            html  
    print.saddle.distn                      html  
    print.simplex                           html  
    remission                               html  
    saddle                                  html  
    saddle.distn                            html  
    saddle.distn.object                     html  
    salinity                                html  
    simplex                                 html  
    simplex.object                          html  
    smooth.f                                html  
    sunspot                                 html  
    survival                                html  
    tau                                     html  
    tilt.boot                               html  
    tsboot                                  html  
    tuna                                    html  
    urine                                   html  
    var.linear                              html  
    wool                                    html  
** building package indices
** testing if installed package can be loaded
* DONE (boot)
Making 'packages.html' ... done
begin installing recommended package cluster
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpZcxgne/R.INSTALL36643c3439e783/cluster/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c clara.c -o clara.o
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c daisy.f -o daisy.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dysta.f -o dysta.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fanny.c -o fanny.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mona.c -o mona.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pam.c -o pam.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sildist.c -o sildist.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c spannel.c -o spannel.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c twins.c -o twins.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpZcxgne/R.INSTALL36643c3439e783/cluster/src'
installing to /builddir/build/BUILD/R-4.1.0/library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cluster'
    finding HTML links ... done
    agnes                                   html  
    agnes.object                            html  
    agriculture                             html  
    animals                                 html  
    bannerplot                              html  
    chorSub                                 html  
    clara                                   html  
    clara.object                            html  
    clusGap                                 html  
    clusplot.default                        html  
    clusplot.partition                      html  
    cluster-internal                        html  
    coef.hclust                             html  
    daisy                                   html  
    diana                                   html  
    dissimilarity.object                    html  
    ellipsoidhull                           html  
    fanny                                   html  
    fanny.object                            html  
    flower                                  html  
    lower.to.upper.tri.inds                 html  
    mona                                    html  
    mona.object                             html  
    pam                                     html  
    pam.object                              html  
    partition.object                        html  
    plantTraits                             html  
    plot.agnes                              html  
    plot.diana                              html  
    plot.mona                               html  
    plot.partition                          html  
    pltree                                  html  
    pluton                                  html  
    predict.ellipsoid                       html  
    print.agnes                             html  
    print.clara                             html  
    print.diana                             html  
    print.dissimilarity                     html  
    print.fanny                             html  
    print.mona                              html  
    print.pam                               html  
    ruspini                                 html  
    silhouette                              html  
    sizeDiss                                html  
    summary.agnes                           html  
    summary.clara                           html  
    summary.diana                           html  
    summary.mona                            html  
    summary.pam                             html  
    twins.object                            html  
    volume.ellipsoid                        html  
    votes.repub                             html  
    xclara                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (cluster)
Making 'packages.html' ... done
begin installing recommended package codetools
* installing *source* package 'codetools' ...
** package 'codetools' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'codetools'
    finding HTML links ... done
    checkUsage                              html  
    codetools                               html  
    findGlobals                             html  
    showTree                                html  
** building package indices
** testing if installed package can be loaded
* DONE (codetools)
Making 'packages.html' ... done
begin installing recommended package foreign
* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpOmRgn5/R.INSTALL3664a752cefdb0/foreign/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c R_systat.c -o R_systat.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Rdbfread.c -o Rdbfread.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c Rdbfwrite.c -o Rdbfwrite.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c SASxport.c -o SASxport.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c avl.c -o avl.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dbfopen.c -o dbfopen.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c file-handle.c -o file-handle.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c format.c -o format.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c minitab.c -o minitab.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pfm-read.c -o pfm-read.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sfm-read.c -o sfm-read.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c spss.c -o spss.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c stataread.c -o stataread.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpOmRgn5/R.INSTALL3664a752cefdb0/foreign/src'
installing to /builddir/build/BUILD/R-4.1.0/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'foreign'
    finding HTML links ... done
    lookup.xport                            html  
    read.S                                  html  
    read.arff                               html  
    read.dbf                                html  
    read.dta                                html  
    read.epiinfo                            html  
    read.mtp                                html  
    read.octave                             html  
    read.spss                               html  
    read.ssd                                html  
    read.systat                             html  
    read.xport                              html  
    write.arff                              html  
    write.dbf                               html  
    write.dta                               html  
    write.foreign                           html  
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
Making 'packages.html' ... done
begin installing recommended package KernSmooth
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpAqA8Ms/R.INSTALL3665001d085f7c/KernSmooth/src'
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c blkest.f -o blkest.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c cp.f -o cp.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dgedi.f -o dgedi.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dgefa.f -o dgefa.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c dgesl.f -o dgesl.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c linbin.f -o linbin.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c linbin2D.f -o linbin2D.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c locpoly.f -o locpoly.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c rlbin.f -o rlbin.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c sdiag.f -o sdiag.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gfortran -m64 -fno-optimize-sibling-calls  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules  -c sstdiag.f -o sstdiag.o
f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpAqA8Ms/R.INSTALL3665001d085f7c/KernSmooth/src'
installing to /builddir/build/BUILD/R-4.1.0/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KernSmooth'
    finding HTML links ... done
    bkde                                    html  
    bkde2D                                  html  
    bkfe                                    html  
    dpih                                    html  
    dpik                                    html  
    dpill                                   html  
    locpoly                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
Making 'packages.html' ... done
begin installing recommended package rpart
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpJc7iAP/R.INSTALL3665501b81cea0/rpart/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c anova.c -o anova.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c anovapred.c -o anovapred.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c branch.c -o branch.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bsplit.c -o bsplit.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c choose_surg.c -o choose_surg.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fix_cp.c -o fix_cp.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c free_tree.c -o free_tree.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gini.c -o gini.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c graycode.c -o graycode.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c insert_split.c -o insert_split.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c make_cp_list.c -o make_cp_list.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c make_cp_table.c -o make_cp_table.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mysort.c -o mysort.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c nodesplit.c -o nodesplit.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c partition.c -o partition.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c poisson.c -o poisson.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pred_rpart.c -o pred_rpart.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c print_tree.c -o print_tree.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpart.c -o rpart.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpart_callback.c -o rpart_callback.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpartexp.c -o rpartexp.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpartexp2.c -o rpartexp2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpcountup.c -o rpcountup.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rpmatrix.c -o rpmatrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rundown.c -o rundown.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c rundown2.c -o rundown2.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c surrogate.c -o surrogate.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c usersplit.c -o usersplit.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c xpred.c -o xpred.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c xval.c -o xval.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpJc7iAP/R.INSTALL3665501b81cea0/rpart/src'
installing to /builddir/build/BUILD/R-4.1.0/library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rpart'
    finding HTML links ... done
    car.test.frame                          html  
    car90                                   html  
    cu.summary                              html  
    kyphosis                                html  
    labels.rpart                            html  
    meanvar.rpart                           html  
    na.rpart                                html  
    path.rpart                              html  
    plot.rpart                              html  
    plotcp                                  html  
    post.rpart                              html  
    predict.rpart                           html  
    print.rpart                             html  
    printcp                                 html  
    prune.rpart                             html  
    residuals.rpart                         html  
    rpart-internal                          html  
    rpart                                   html  
    rpart.control                           html  
    rpart.exp                               html  
    rpart.object                            html  
    rsq.rpart                               html  
    snip.rpart                              html  
    solder.balance                          html  
    stagec                                  html  
    summary.rpart                           html  
    text.rpart                              html  
    xpred.rpart                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done
begin installing recommended package class
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmpX11OLB/R.INSTALL3665d91cc6c0d/class/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c class.c -o class.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o class.so class.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmpX11OLB/R.INSTALL3665d91cc6c0d/class/src'
installing to /builddir/build/BUILD/R-4.1.0/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'class'
    finding HTML links ... done
    SOM                                     html  
    batchSOM                                html  
    condense                                html  
    knn                                     html  
    knn.cv                                  html  
    knn1                                    html  
    lvq1                                    html  
    lvq2                                    html  
    lvq3                                    html  
    lvqinit                                 html  
    lvqtest                                 html  
    multiedit                               html  
    olvq1                                   html  
    reduce.nn                               html  
    somgrid                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (class)
Making 'packages.html' ... done
begin installing recommended package nnet
* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/Rtmpfb8CHI/R.INSTALL36660831787865/nnet/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c nnet.c -o nnet.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o nnet.so nnet.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/Rtmpfb8CHI/R.INSTALL36660831787865/nnet/src'
installing to /builddir/build/BUILD/R-4.1.0/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nnet'
    finding HTML links ... done
    class.ind                               html  
    multinom                                html  
    nnet.Hess                               html  
    nnet                                    html  
    predict.nnet                            html  
    which.is.max                            html  
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
begin installing recommended package spatial
* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/Rtmp4uLsRn/R.INSTALL3666373916fb0/spatial/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c krc.c -o krc.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pps.c -o pps.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o spatial.so init.o krc.o pps.o -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/Rtmp4uLsRn/R.INSTALL3666373916fb0/spatial/src'
installing to /builddir/build/BUILD/R-4.1.0/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spatial'
    finding HTML links ... done
    Kaver                                   html  
    Kenvl                                   html  
    Kfn                                     html  
    Psim                                    html  
    SSI                                     html  
    Strauss                                 html  
    anova.trls                              html  
    correlogram                             html  
    expcov                                  html  
    ppgetregion                             html  
    ppinit                                  html  
    pplik                                   html  
    ppregion                                html  
    predict.trls                            html  
    prmat                                   html  
    semat                                   html  
    surf.gls                                html  
    surf.ls                                 html  
    trls.influence                          html  
    trmat                                   html  
    variogram                               html  
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
Making 'packages.html' ... done
begin installing recommended package mgcv
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
make[3]: Entering directory '/tmp/RtmponZqZw/R.INSTALL36666c55133bef/mgcv/src'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c coxph.c -o coxph.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c davies.c -o davies.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c discrete.c -o discrete.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gdi.c -o gdi.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.c -o init.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c magic.c -o magic.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mat.c -o mat.o
mat.c: In function 'Rlanczos':
mat.c:3622:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 3622 |   for (i=0;i< *n+1;i++) if (q[i]) FREE(q[i]);FREE(q);
      |   ^~~
In file included from mat.c:50:
mgcv.h:62:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
   62 | #define FREE R_chk_free
      |              ^~~~~~~~~~
mat.c:3622:46: note: in expansion of macro 'FREE'
 3622 |   for (i=0;i< *n+1;i++) if (q[i]) FREE(q[i]);FREE(q);
      |                                              ^~~~
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c matrix.c -o matrix.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mgcv.c -o mgcv.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c misc.c -o misc.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c mvn.c -o mvn.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c qp.c -o qp.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c soap.c -o soap.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sparse-smooth.c -o sparse-smooth.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c sparse.c -o sparse.o
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c tprs.c -o tprs.o
gcc -m64 -shared -L/builddir/build/BUILD/R-4.1.0/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -lopenblas -lgfortran -lm -lquadmath -fopenmp -L/builddir/build/BUILD/R-4.1.0/lib -lR
make[3]: Leaving directory '/tmp/RtmponZqZw/R.INSTALL36666c55133bef/mgcv/src'
installing to /builddir/build/BUILD/R-4.1.0/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mgcv'
    finding HTML links ... done
    Beta                                    html  
    FFdes                                   html  
    Predict.matrix                          html  
    Predict.matrix.cr.smooth                html  
    Predict.matrix.soap.film                html  
    Rrank                                   html  
    Sl.initial.repara                       html  
    Sl.repara                               html  
    Sl.setup                                html  
    Tweedie                                 html  
    XWXd                                    html  
    anova.gam                               html  
    bam                                     html  
    bam.update                              html  
    bandchol                                html  
    blas.thread.test                        html  
    bug.reports.mgcv                        html  
    cSplineDes                              html  
    chol.down                               html  
    choose.k                                html  
    columb                                  html  
    concurvity                              html  
    coxph                                   html  
    coxpht                                  html  
    dDeta                                   html  
    exclude.too.far                         html  
    extract.lme.cov                         html  
    family.mgcv                             html  
    fix.family.link                         html  
    fixDependence                           html  
    formXtViX                               html  
    formula.gam                             html  
    fs.test                                 html  
    full.score                              html  
    gam                                     html  
    gam.check                               html  
    gam.control                             html  
    gam.convergence                         html  
    gam.fit                                 html  
    gam.fit3                                html  
    gam.fit5.post.proc                      html  
    gam.mh                                  html  
    gam.models                              html  
    gam.outer                               html  
    gam.reparam                             html  
    gam.scale                               html  
    gam.selection                           html  
    gam.side                                html  
    gam.vcomp                               html  
    gam2objective                           html  
    gamObject                               html  
    gamSim                                  html  
    gamlss.etamu                            html  
    gamlss.gH                               html  
    gamm                                    html  
    gammals                                 html  
    gaulss                                  html  
    get.var                                 html  
    gevlss                                  html  
    ginla                                   html  
    gumbls                                  html  
    identifiability                         html  
    in.out                                  html  
    inSide                                  html  
    influence.gam                           html  
    initial.sp                              html  
    interpret.gam                           html  
    jagam                                   html  
    k.check                                 html  
    ldTweedie                               html  
    ldetS                                   html  
    linear.functional.terms                 html  
    logLik.gam                              html  
    ls.size                                 html  
    magic                                   html  
    magic.post.proc                         html  
    mgcv-FAQ                                html  
    mgcv-package                            html  
    mgcv-parallel                           html  
    mini.roots                              html  
    missing.data                            html  
    model.matrix.gam                        html  
    mono.con                                html  
    mroot                                   html  
    multinom                                html  
    mvn                                     html  
    negbin                                  html  
    new.name                                html  
    notExp                                  html  
    notExp2                                 html  
    null.space.dimension                    html  
    ocat                                    html  
    one.se.rule                             html  
    pcls                                    html  
    pdIdnot                                 html  
    pdTens                                  html  
    pen.edf                                 html  
    place.knots                             html  
    plot.gam                                html  
    polys.plot                              html  
    predict.bam                             html  
    predict.gam                             html  
    print.gam                               html  
    psum.chisq                              html  
    qq.gam                                  html  
    rTweedie                                html  
    random.effects                          html  
    residuals.gam                           html  
    rig                                     html  
    rmvn                                    html  
    s                                       html  
    scat                                    html  
    sdiag                                   html  
    shash                                   html  
    single.index                            html  
    slanczos                                html  
    smooth.construct                        html  
    smooth.construct.ad.smooth.spec         html  
    smooth.construct.bs.smooth.spec         html  
    smooth.construct.cr.smooth.spec         html  
    smooth.construct.ds.smooth.spec         html  
    smooth.construct.fs.smooth.spec         html  
    smooth.construct.gp.smooth.spec         html  
    smooth.construct.mrf.smooth.spec        html  
    smooth.construct.ps.smooth.spec         html  
    smooth.construct.re.smooth.spec         html  
    smooth.construct.so.smooth.spec         html  
    smooth.construct.sos.smooth.spec        html  
    smooth.construct.t2.smooth.spec         html  
    smooth.construct.tensor.smooth.spec     html  
    smooth.construct.tp.smooth.spec         html  
    smooth.info                             html  
    smooth.terms                            html  
    smooth2random                           html  
    smoothCon                               html  
    sp.vcov                                 html  
    spasm.construct                         html  
    step.gam                                html  
    summary.gam                             html  
    t2                                      html  
    te                                      html  
    tensor.prod.model.matrix                html  
    totalPenaltySpace                       html  
    trichol                                 html  
    trind.generator                         html  
    twlss                                   html  
    uniquecombs                             html  
    vcov.gam                                html  
    vis.gam                                 html  
    ziP                                     html  
    ziplss                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
Making 'packages.html' ... done
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/Recommended'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library/Recommended'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/library'
building/updating vignettes for package 'grid' ...
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
building/updating vignettes for package 'stats' ...
processing 'reshape.Rnw'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/library'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0'
configuring Java ...
Java interpreter : /usr/bin/java
Java version     : 11.0.12
Java home path   : /usr/lib/jvm/java-11-openjdk-11.0.12.0.7-0.eln112.x86_64
Java compiler    : not present
Java headers gen.: 
Java archive tool: 
trying to compile and link a JNI program 
detected JNI cpp flags    : 
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
make[2]: Entering directory '/tmp/Rjavareconf.EXqnkX'
gcc -m64 -I"/builddir/build/BUILD/R-4.1.0/include" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: jni.h: No such file or directory
    1 | #include <jni.h>
      |          ^~~~~~~
compilation terminated.
make[2]: *** [/builddir/build/BUILD/R-4.1.0/etc/Makeconf:168: conftest.o] Error 1
make[2]: Leaving directory '/tmp/Rjavareconf.EXqnkX'
Unable to compile a JNI program
JAVA_HOME        : /usr/lib/jvm/java-11-openjdk-11.0.12.0.7-0.eln112.x86_64
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /builddir/build/BUILD/R-4.1.0
Done.
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0'
+ cd src/nmath/standalone
+ make
(cd ../../include; make Rmath.h)
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/include'
make[1]: 'Rmath.h' is up to date.
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/include'
Copying source files
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/nmath/standalone'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
making std_unif.d from std_unif.c
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/nmath/standalone'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/nmath/standalone'
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mlutils.c -o mlutils.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c d1mach.c -o d1mach.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c i1mach.c -o i1mach.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fmax2.c -o fmax2.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fmin2.c -o fmin2.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fprec.c -o fprec.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fround.c -o fround.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ftrunc.c -o ftrunc.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sign.c -o sign.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fsign.c -o fsign.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c imax2.c -o imax2.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c imin2.c -o imin2.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c chebyshev.c -o chebyshev.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c log1p.c -o log1p.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lgammacor.c -o lgammacor.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gammalims.c -o gammalims.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c stirlerr.c -o stirlerr.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bd0.c -o bd0.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gamma.c -o gamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lgamma.c -o lgamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gamma_cody.c -o gamma_cody.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c beta.c -o beta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lbeta.c -o lbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c polygamma.c -o polygamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cospi.c -o cospi.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_i.c -o bessel_i.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_j.c -o bessel_j.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_k.c -o bessel_k.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_y.c -o bessel_y.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c choose.c -o choose.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c snorm.c -o snorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sexp.c -o sexp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dgamma.c -o dgamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pgamma.c -o pgamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qgamma.c -o qgamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rgamma.c -o rgamma.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dbeta.c -o dbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pbeta.c -o pbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qbeta.c -o qbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rbeta.c -o rbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dunif.c -o dunif.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c punif.c -o punif.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qunif.c -o qunif.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c runif.c -o runif.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnorm.c -o dnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnorm.c -o pnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnorm.c -o qnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rnorm.c -o rnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dlnorm.c -o dlnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plnorm.c -o plnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qlnorm.c -o qlnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlnorm.c -o rlnorm.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c df.c -o df.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pf.c -o pf.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qf.c -o qf.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rf.c -o rf.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnf.c -o dnf.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dt.c -o dt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pt.c -o pt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qt.c -o qt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rt.c -o rt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnt.c -o dnt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dchisq.c -o dchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pchisq.c -o pchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qchisq.c -o qchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rchisq.c -o rchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rnchisq.c -o rnchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dbinom.c -o dbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pbinom.c -o pbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qbinom.c -o qbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rbinom.c -o rbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rmultinom.c -o rmultinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dcauchy.c -o dcauchy.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pcauchy.c -o pcauchy.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qcauchy.c -o qcauchy.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rcauchy.c -o rcauchy.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dexp.c -o dexp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pexp.c -o pexp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qexp.c -o qexp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rexp.c -o rexp.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dgeom.c -o dgeom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pgeom.c -o pgeom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qgeom.c -o qgeom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rgeom.c -o rgeom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dhyper.c -o dhyper.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c phyper.c -o phyper.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qhyper.c -o qhyper.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rhyper.c -o rhyper.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnbinom.c -o dnbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnbinom.c -o pnbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnbinom.c -o qnbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rnbinom.c -o rnbinom.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dpois.c -o dpois.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ppois.c -o ppois.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qpois.c -o qpois.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rpois.c -o rpois.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dweibull.c -o dweibull.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pweibull.c -o pweibull.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qweibull.c -o qweibull.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rweibull.c -o rweibull.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dlogis.c -o dlogis.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plogis.c -o plogis.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qlogis.c -o qlogis.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlogis.c -o rlogis.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnchisq.c -o dnchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnchisq.c -o pnchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnchisq.c -o qnchisq.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnbeta.c -o dnbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnbeta.c -o pnbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnbeta.c -o qnbeta.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnf.c -o pnf.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnt.c -o pnt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnf.c -o qnf.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnt.c -o qnt.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ptukey.c -o ptukey.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qtukey.c -o qtukey.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c toms708.c -o toms708.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c wilcox.c -o wilcox.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c signrank.c -o signrank.o
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c std_unif.c -o std_unif.o
ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o
ranlib libRmath.a
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/nmath/standalone'
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/nmath/standalone'
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mlutils.c -o mlutils.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c d1mach.c -o d1mach.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c i1mach.c -o i1mach.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fmax2.c -o fmax2.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fmin2.c -o fmin2.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fprec.c -o fprec.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fround.c -o fround.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ftrunc.c -o ftrunc.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sign.c -o sign.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c fsign.c -o fsign.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c imax2.c -o imax2.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c imin2.c -o imin2.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c chebyshev.c -o chebyshev.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c log1p.c -o log1p.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lgammacor.c -o lgammacor.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gammalims.c -o gammalims.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c stirlerr.c -o stirlerr.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bd0.c -o bd0.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gamma.c -o gamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lgamma.c -o lgamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gamma_cody.c -o gamma_cody.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c beta.c -o beta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lbeta.c -o lbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c polygamma.c -o polygamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cospi.c -o cospi.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_i.c -o bessel_i.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_j.c -o bessel_j.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_k.c -o bessel_k.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c bessel_y.c -o bessel_y.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c choose.c -o choose.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c snorm.c -o snorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sexp.c -o sexp.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dgamma.c -o dgamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pgamma.c -o pgamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qgamma.c -o qgamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rgamma.c -o rgamma.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dbeta.c -o dbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pbeta.c -o pbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qbeta.c -o qbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rbeta.c -o rbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dunif.c -o dunif.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c punif.c -o punif.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qunif.c -o qunif.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c runif.c -o runif.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnorm.c -o dnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnorm.c -o pnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnorm.c -o qnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rnorm.c -o rnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dlnorm.c -o dlnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plnorm.c -o plnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qlnorm.c -o qlnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlnorm.c -o rlnorm.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c df.c -o df.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pf.c -o pf.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qf.c -o qf.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rf.c -o rf.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnf.c -o dnf.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dt.c -o dt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pt.c -o pt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qt.c -o qt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rt.c -o rt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnt.c -o dnt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dchisq.c -o dchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pchisq.c -o pchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qchisq.c -o qchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rchisq.c -o rchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rnchisq.c -o rnchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dbinom.c -o dbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pbinom.c -o pbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qbinom.c -o qbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rbinom.c -o rbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rmultinom.c -o rmultinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dcauchy.c -o dcauchy.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pcauchy.c -o pcauchy.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qcauchy.c -o qcauchy.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rcauchy.c -o rcauchy.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dexp.c -o dexp.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pexp.c -o pexp.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qexp.c -o qexp.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rexp.c -o rexp.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dgeom.c -o dgeom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pgeom.c -o pgeom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qgeom.c -o qgeom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rgeom.c -o rgeom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dhyper.c -o dhyper.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c phyper.c -o phyper.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qhyper.c -o qhyper.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rhyper.c -o rhyper.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnbinom.c -o dnbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnbinom.c -o pnbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnbinom.c -o qnbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rnbinom.c -o rnbinom.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dpois.c -o dpois.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ppois.c -o ppois.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qpois.c -o qpois.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rpois.c -o rpois.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dweibull.c -o dweibull.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pweibull.c -o pweibull.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qweibull.c -o qweibull.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rweibull.c -o rweibull.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dlogis.c -o dlogis.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plogis.c -o plogis.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qlogis.c -o qlogis.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlogis.c -o rlogis.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnchisq.c -o dnchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnchisq.c -o pnchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnchisq.c -o qnchisq.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dnbeta.c -o dnbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnbeta.c -o pnbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnbeta.c -o qnbeta.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnf.c -o pnf.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pnt.c -o pnt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnf.c -o qnf.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnt.c -o qnt.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ptukey.c -o ptukey.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qtukey.c -o qtukey.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c toms708.c -o toms708.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c wilcox.c -o wilcox.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c signrank.c -o signrank.lo
gcc -m64 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE   -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c std_unif.c -o std_unif.lo
gcc -m64 -shared -fopenmp -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -o libRmath.so  mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm
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Chapter 1.
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-
wise, it is \T1/pcr/m/n/10 (double.base ^
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
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\T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt
m/m/n/10 if \T1/pcr/m/n/10 double.base
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\T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/pcr/m/n/10 (double.base
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\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
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[]\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]("long.double") \T1/
ptm/m/n/10 is true, there are 10 such
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\T1/pcr/m/n/10 *.exponent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 *.min.exp\T1/ptm/m/n/1
0 , and \T1/pcr/m/n/10 *.max.exp\T1/ptm/m/n/10 , com-puted en-tirely anal-o-gou
sly to their
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
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rel.diff.=",[] 
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
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pty.names = TRUE,[] 
[28]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[29] [30]
Underfull \hbox (badness 10000) in paragraph at lines 1908--1910
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[31] [32]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
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[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[33] [34] [35] [36]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[37]
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 []  \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo
ne1970.tab"),[] 
[38]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
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[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[39]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[40] [41] [42]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2730--2730
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE), 
[43] [44] [45] [46] [47] [48] [49] [50] [51]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3399--3399
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 
[52]
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 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 
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 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
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 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 
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 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
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 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[53] [54] [55] [56] [57] [58]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[59] [60] [61] [62] [63] [64] [65]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
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\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[66] [67]
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 []             \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[] 
[68]
Underfull \hbox (badness 4595) in paragraph at lines 4542--4545
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[69] [70]
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 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
[71]
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[72] [73]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[74] [75] [76] [77]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[78] [79] [80] [81] [82] [83]
Underfull \hbox (badness 10000) in paragraph at lines 5600--5608
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[84] [85] [86] [87] [88] [89] [90] [91] [92]
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[93] [94] [95]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6371--6371
 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows  \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] 
[96] [97]
Underfull \hbox (badness 1635) in paragraph at lines 6573--6576
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing
[98]
Underfull \hbox (badness 1308) in paragraph at lines 6620--6628
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[99] [100]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6784--6784
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[101]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6836--6838
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
[102] [103]
Underfull \hbox (badness 1997) in paragraph at lines 6972--6977
[]\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1
0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x
zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC
onnection\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 7010--7013
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[104] [105] [106]
Underfull \hbox (badness 1406) in paragraph at lines 7192--7198
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
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\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and 
web-pages gen-er-ated by
Underfull \hbox (badness 2134) in paragraph at lines 7192--7198
\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 7192--7198
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 7212--7214
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/pcr/m/n/10 descriptio
n = "clipboard" \T1/ptm/m/n/10 in mode \T1/pcr/m/n/10 "r" \T1/ptm/m/n/10 only. 
This
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\T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http
s : / / specifications . freedesktop .
Underfull \hbox (badness 1735) in paragraph at lines 7254--7261
\T1/pcr/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as \
T1/pcr/m/n/10 "X11_secondary"\T1/ptm/m/n/10 . On most sys-
[107] [108]
Underfull \vbox (badness 10000) has occurred while \output is active [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[111]
Underfull \hbox (badness 1231) in paragraph at lines 7583--7589
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[112] [113] [114]
Underfull \hbox (badness 10000) in paragraph at lines 7795--7797
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[115] [116] [117]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7954--7954
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[118] [119] [120] [121]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8187--8187
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[122]
Underfull \hbox (badness 10000) in paragraph at lines 8306--8316
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8306--8316
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be
[123]
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[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[124] [125]
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 []                 \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[] 
[126] [127] [128] [129]
Underfull \hbox (badness 1629) in paragraph at lines 8829--8841
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8829--8841
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[130] [131] [132] [133] [134] [135]
Underfull \hbox (badness 10000) in paragraph at lines 9278--9282
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[136] [137]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9371--9371
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9397--9397
 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
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 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[138] [139]
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[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9554--9556
[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[140] [141] [142]
Underfull \hbox (badness 1603) in paragraph at lines 9779--9782
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[143] [144] [145] [146] [147] [148] [149] [150] [151]
Underfull \hbox (badness 1917) in paragraph at lines 10394--10399
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[152]
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 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10450--10450
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[153] [154]
Underfull \hbox (badness 1168) in paragraph at lines 10552--10557
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
Underfull \hbox (badness 10000) in paragraph at lines 10592--10598
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
[155] [156]
Underfull \hbox (badness 2828) in paragraph at lines 10769--10774
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10769--10774
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
[157]
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 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[158]
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 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] 
[159] [160]
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 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[161] [162] [163]
Underfull \hbox (badness 6396) in paragraph at lines 11218--11226
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[164] [165] [166]
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[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[167] [168] [169] [170] [171] [172] [173]
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 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[] 
[174] [175] [176]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
Underfull \hbox (badness 3039) in paragraph at lines 12160--12165
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
[177]
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[178] [179]
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment
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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[180] [181]
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13328--13328
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[193] [194] [195] [196] [197] [198] [199]
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\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
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\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[200] [201] [202]
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[203] [204]
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[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr
/m/n/10 fsep =
[205] [206]
Underfull \hbox (badness 10000) in paragraph at lines 14331--14333
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[207] [208]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14459--14462
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[209]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[210]
Underfull \hbox (badness 10000) in paragraph at lines 14599--14602
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14609--14609
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14675--14678
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class
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 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[212]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14745--14752
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14753--14757
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[213] [214] [215]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14918--14918
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[216] [217] [218]
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 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15155--15155
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[219]
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[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[220]
Underfull \hbox (badness 6944) in paragraph at lines 15337--15340
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[221]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[222] [223]
Underfull \hbox (badness 10000) in paragraph at lines 15500--15502
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[224]
Underfull \hbox (badness 2790) in paragraph at lines 15533--15536
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
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[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[225]
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[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls
Underfull \hbox (badness 4954) in paragraph at lines 15639--15641
\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this
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[]\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
[226]
Underfull \hbox (badness 10000) in paragraph at lines 15673--15677
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
Underfull \hbox (badness 10000) in paragraph at lines 15673--15677
\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 15678--15686
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15786--15786
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [228]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 15808--15808
 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you 
want see the effect[] 
[229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16642--16642
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[241]
Underfull \hbox (badness 2418) in paragraph at lines 16751--16755
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 6510) in paragraph at lines 16758--16761
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
[242]
Underfull \hbox (badness 2326) in paragraph at lines 16793--16800
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[243] [244] [245]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17050--17050
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
[246]
Underfull \hbox (badness 1867) in paragraph at lines 17078--17085
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[247] [248] [249] [250]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17379--17379
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
Underfull \vbox (badness 10000) has occurred while \output is active [251]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 17408--17408
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
[252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17464--17464
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[253] [254] [255] [256]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17837--17837
 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9))) 
[257]
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 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[] 
[258] [259] [260]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18092--18092
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[261] [262] [263] [264]
Underfull \hbox (badness 2285) in paragraph at lines 18426--18428
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
[265]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18434--18434
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[266] [267]
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 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
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 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
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 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18612--18612
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[268] [269]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 18739--18739
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
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 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] 
[270] [271] [272]
Underfull \hbox (badness 10000) in paragraph at lines 18952--18954
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[273] [274] [275] [276] [277]
Underfull \hbox (badness 10000) in paragraph at lines 19290--19296
Underfull \hbox (badness 10000) in paragraph at lines 19303--19305
[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[278] [279] [280]
Underfull \hbox (badness 4699) in paragraph at lines 19535--19538
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[281] [282]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19663--19663
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[283] [284] [285]
Underfull \hbox (badness 4739) in paragraph at lines 19798--19800
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[286]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 19847--19847
 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19848--19848
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[287] [288] [289] [290] [291] [292] [293] [294]
Underfull \hbox (badness 1975) in paragraph at lines 20459--20462
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[295] [296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1077) in paragraph at lines 20857--20862
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 20871--20878
[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
[302]
Underfull \hbox (badness 10000) in paragraph at lines 20951--20955
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-
Underfull \hbox (badness 10000) in paragraph at lines 20951--20955
\T1/ptm/m/n/10 tory `\T1/pcr/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/pcr
/m/n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (o
r
[303] [304]
Underfull \hbox (badness 10000) in paragraph at lines 21100--21104
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
Underfull \hbox (badness 1454) in paragraph at lines 21100--21104
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-
[305] [306]
Underfull \hbox (badness 10000) in paragraph at lines 21236--21243
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21357--21361
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[309]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 21427--21432
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21427--21432
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[310] [311]
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[312]
Underfull \hbox (badness 3343) in paragraph at lines 21659--21663
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[313] [314]
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 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
[315]
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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 prob = 0.2))),[] 
[316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21922--21922
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21925--21925
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
[317]
Underfull \hbox (badness 6380) in paragraph at lines 21970--21975
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[318]
Underfull \hbox (badness 2564) in paragraph at lines 22061--22064
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[319]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 22098--22098
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[320] [321]
Underfull \hbox (badness 1400) in paragraph at lines 22266--22270
[][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][]
 \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do
uble[][][] \T1/ptm/m/n/10 (class
[322] [323]
Underfull \hbox (badness 1824) in paragraph at lines 22436--22444
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. In nu-meric and
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\T1/ptm/m/n/10 com-plex vec-tors, ze-ros are \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/1
0 and non-zero val-ues are \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 . For [][]\T1/pcr/
m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 10000) in paragraph at lines 22436--22444
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
Underfull \hbox (badness 4531) in paragraph at lines 22436--22444
\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 23093--23093
 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary =  r ), complex(real =  
r , imaginary = NA ),[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 23094--23094
 []        \T1/pcr/m/n/9 complex(real =  r , imaginary = NaN), complex(real = N
aN, imaginary =  r ))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 23097--23097
 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] 
[334] [335]
Underfull \hbox (badness 1655) in paragraph at lines 23221--23225
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[336] [337] [338] [339]
Underfull \hbox (badness 2277) in paragraph at lines 23470--23473
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
 \T1/ptm/m/n/10 are typ-i-cally prefer-able.
[340] [341]
Underfull \hbox (badness 10000) in paragraph at lines 23601--23604
[]\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc
r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.
0,
[342] [343] [344] [345] [346] [347] [348]
Underfull \hbox (badness 1484) in paragraph at lines 24057--24065
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less 
the OS's de-fault has been
Underfull \hbox (badness 1152) in paragraph at lines 24057--24065
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[349]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24135--24135
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[350] [351] [352] [353] [354] [355] [356]
Underfull \hbox (badness 1448) in paragraph at lines 24648--24656
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[357] [358]
Underfull \hbox (badness 3849) in paragraph at lines 24763--24768
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[359]
Underfull \hbox (badness 7308) in paragraph at lines 24840--24846
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 10000) in paragraph at lines 24840--24846
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) 
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 1210) in paragraph at lines 24840--24846
[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 
. If the en-vi-ron-ment is used as a hash
Underfull \hbox (badness 10000) in paragraph at lines 24850--24853
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 24850--24853
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[360] [361]
Underfull \hbox (badness 10000) in paragraph at lines 25003--25005
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[362] [363] [364]
Underfull \hbox (badness 6188) in paragraph at lines 25225--25228
[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[365] [366] [367]
Underfull \hbox (badness 1521) in paragraph at lines 25410--25424
\T1/ptm/m/n/10 tion \T1/pcr/m/n/10 GetFinalPathNameByHandle \T1/ptm/m/n/10 and 
in case of an er-ror (such as in-suf-fi-cient per-
[368] [369] [370] [371] [372]
Underfull \hbox (badness 2197) in paragraph at lines 25724--25728
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
Underfull \hbox (badness 4048) in paragraph at lines 25724--25728
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
Underfull \hbox (badness 2846) in paragraph at lines 25738--25742
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-
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\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
Overfull \hbox (12.78088pt too wide) in paragraph at lines 25780--25780
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 
[373]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25784--25784
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[374]
Underfull \hbox (badness 10000) in paragraph at lines 25832--25838
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 25832--25838
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
Underfull \hbox (badness 10000) in paragraph at lines 25845--25847
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
[375]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25912--25912
 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] 
[376] [377]
Underfull \hbox (badness 8189) in paragraph at lines 26107--26113
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][]
[378] [379] [380]
Underfull \hbox (badness 1694) in paragraph at lines 26332--26335
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[381] [382] [383] [384]
Underfull \hbox (badness 1603) in paragraph at lines 26579--26581
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[385] [386]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 26706--26714
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[387] [388]
Underfull \hbox (badness 3271) in paragraph at lines 26925--26928
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[389] [390] [391]
Underfull \hbox (badness 3138) in paragraph at lines 27231--27237
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 27231--27237
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 2088) in paragraph at lines 27231--27237
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by
[392]
Underfull \hbox (badness 1194) in paragraph at lines 27244--27247
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and
Underfull \hbox (badness 1389) in paragraph at lines 27270--27272
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
Underfull \hbox (badness 3826) in paragraph at lines 27305--27310
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Underfull \hbox (badness 1009) in paragraph at lines 27323--27326
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[393]
Underfull \hbox (badness 10000) in paragraph at lines 27339--27342
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27347--27353
\T1/ptm/m/n/10 build), \T1/pcr/m/n/10 "mac.binary" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27347--27353
\T1/ptm/m/n/10 builds). (\T1/pcr/m/n/10 "mac.binary.el-capitan"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5091) in paragraph at lines 27347--27353
\T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina
ry.universal" \T1/ptm/m/n/10 are no longer
Underfull \hbox (badness 10000) in paragraph at lines 27362--27369
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 2384) in paragraph at lines 27362--27369
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 27362--27369
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke \T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 27362--27369
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[394] [395] [396] [397]
Underfull \vbox (badness 10000) has occurred while \output is active [398]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27710--27710
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 
Underfull \hbox (badness 10000) in paragraph at lines 27723--27727
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
Underfull \hbox (badness 10000) in paragraph at lines 27723--27727
\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[399] [400]
Underfull \hbox (badness 10000) in paragraph at lines 27870--27873
[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
Underfull \hbox (badness 1062) in paragraph at lines 27870--27873
\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 28152--28158
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Underfull \hbox (badness 2495) in paragraph at lines 28152--28158
[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
 \T1/ptm/m/n/10 which con-cate-nates and
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 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28186--28186
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
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 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
 ' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling :
[] 
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 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[] 
[405] [406] [407]
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 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow()  # same as nrow(subset(mt
cars, cyl == 4))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28386--28386
 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so 
is not evaluated[] 
[408]
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[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type =
[409] [410] [411] [412] [413] [414]
Underfull \hbox (badness 2005) in paragraph at lines 28836--28840
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/cmtt/m/n/10 `\T1/pc
r/m/n/10 name\TS1/cmtt/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr
/m/n/10 get[][][](name,envir =
[415]
Underfull \hbox (badness 1796) in paragraph at lines 28904--28907
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[416] [417] [418] [419]
Underfull \hbox (badness 10000) in paragraph at lines 29108--29111
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 29803--29803
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[430] [431] [432] [433]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30094--30094
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30105--30105
 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 30111--30111
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
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 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
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 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [434]
[435]
Underfull \hbox (badness 7415) in paragraph at lines 30200--30204
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
Overfull \hbox (42.18039pt too wide) in paragraph at lines 30221--30221
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[436]
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 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[437]
Underfull \hbox (badness 3713) in paragraph at lines 30390--30401
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[438] [439]
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\T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM
 Trans-ac-tions on Mod-el-ing and Com-puter
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\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh
ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
[440] [441]
Underfull \hbox (badness 1533) in paragraph at lines 30652--30655
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[442] [443]
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 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[444] [445]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30959--30959
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 30961--30961
 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 
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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 
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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 
[446]
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 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[447] [448] [449] [450]
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 []\T1/pcr/m/n/9 ## Bit representation  [ sign | exponent | mantissa ] of doubl
e prec numbers :[] 
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 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
 # split one double[] 
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 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31292--31292
 []\T1/pcr/m/n/9 d2b  <- function(x) vapply(as.double(x), function(x)          
 numToBits(x) , raw(64L))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [451]
[452]
Underfull \hbox (badness 4048) in paragraph at lines 31387--31392
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:
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\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2080) in paragraph at lines 31924--31934
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 infoRDS\T1/ptm/m/n/10 , an \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 list with el-e-ments \T1/pcr/m/n/10 version \T1/ptm/m/n/10 (ver
-sion num-ber, cur-rently 2 or 3),
Overfull \hbox (4.38043pt too wide) in paragraph at lines 31958--31958
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 7558) in paragraph at lines 32477--32481
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 32487--32489
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
Underfull \hbox (badness 10000) in paragraph at lines 32498--32500
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / 
pubs . opengroup . org / onlinepubs /
[468]
Underfull \hbox (badness 1975) in paragraph at lines 32501--32505
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 pcre2pattern \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 pcrepattern man \T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m/n/10 ht
tps : / / www .
[469] [470] [471] [472] [473]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32872--32872
 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3)         # length 24, 3 complete 
replications[] 
[474]
Underfull \hbox (badness 10000) in paragraph at lines 32943--32947
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[475] [476] [477]
Underfull \hbox (badness 2302) in paragraph at lines 33169--33174
[]\T1/pcr/m/n/10 signif \T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-me
nt to the spec-i-fied num-ber of sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for \T1/pcr/m/n/10 numeric x\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 signif(x,dig) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 round(x,
dig
[478] [479]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33302--33302
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33305--33305
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[480] [481] [482] [483] [484] [485] [486]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 33746--33746
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[487] [488] [489] [490] [491] [492]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34183--34183
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[493] [494]
Underfull \hbox (badness 1158) in paragraph at lines 34287--34292
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
Underfull \hbox (badness 10000) in paragraph at lines 34314--34320
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1762) in paragraph at lines 34314--34320
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions
[495] [496]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 34472--34472
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[497] [498] [499]
Underfull \hbox (badness 8151) in paragraph at lines 34732--34735
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 .
[500] [501] [502] [503]
Underfull \hbox (badness 10000) in paragraph at lines 34947--34952
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10
 gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by =
[504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515]
[516] [517] [518]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 35936--35936
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[519] [520] [521]
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 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
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 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[522]
Underfull \hbox (badness 4954) in paragraph at lines 36233--36239
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 36233--36239
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[523] [524]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36344--36344
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[525] [526] [527] [528] [529]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36685--36685
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36700--36700
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[530] [531] [532]
Underfull \hbox (badness 10000) in paragraph at lines 36925--36927
[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
[533] [534] [535]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 37152--37152
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
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 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[536] [537] [538] [539]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 37420--37420
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[540]
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[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
 saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert 
a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 37511--37521
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an 
en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-
ing
[541]
Underfull \hbox (badness 10000) in paragraph at lines 37557--37563
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 37557--37563
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 37557--37563
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 37572--37579
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 37572--37579
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[542] [543] [544]
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[]\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/
m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[545]
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 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[546] [547] [548] [549] [550] [551] [552] [553] [554]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 38446--38446
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[555] [556] [557]
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 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[558]
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 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[559] [560] [561] [562] [563] [564]
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 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 
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 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[565]
Underfull \hbox (badness 10000) in paragraph at lines 39228--39235
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
Underfull \hbox (badness 10000) in paragraph at lines 39228--39235
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
[566]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39281--39281
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[567] [568] [569] [570] [571]
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 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[572] [573]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39757--39757
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[574]
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 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
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[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 39825--39831
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the \T1/pcr/m/n/10 glob \T1/ptm/m/n/10 sys-tem call.
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[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
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\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[575] [576] [577] [578]
Underfull \hbox (badness 10000) in paragraph at lines 40132--40136
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
[579]
Underfull \hbox (badness 1584) in paragraph at lines 40147--40150
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[580] [581]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 40285--40285
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[582]
Overfull \hbox (19.22812pt too wide) in paragraph at lines 40362--40362
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[583] [584]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[585] [586] [587]
Underfull \hbox (badness 1038) in paragraph at lines 40697--40700
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[588] [589] [590] [591] [592]
Underfull \hbox (badness 1442) in paragraph at lines 41061--41065
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout =
 TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout =
[593] [594] [595] [596]
Underfull \hbox (badness 4096) in paragraph at lines 41311--41314
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[597]
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[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
 length(bin) >
[598] [599] [600]
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 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (35.4281pt too wide) in paragraph at lines 41581--41581
 []            \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[
] 
Overfull \hbox (55.67578pt too wide) in paragraph at lines 41583--41583
 []                 \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = 
NULL), dim=4, dimnames=list(as.character(2:5)))))[] 
Underfull \hbox (badness 10000) in paragraph at lines 41596--41598
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[601]
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[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[602] [603]
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[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[604]
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[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[605] [606] [607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 42283--42290
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 42339--42348
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
[611]
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\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 
' in that di-rec-tory states the ver-sion. That op-tion is
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\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
[612]
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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
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[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
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 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[613] [614] [615]
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[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[616] [617]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42841--42841
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
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 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
[618] [619]
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 []                                           \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[] 
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 []                                           \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[] 
[620] [621] [622]
Underfull \hbox (badness 6542) in paragraph at lines 43220--43222
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[623] [624]
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 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[625]
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[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 43407--43415
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
[626]
Underfull \hbox (badness 4859) in paragraph at lines 43437--43442
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[627]
Underfull \hbox (badness 3895) in paragraph at lines 43499--43511
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 43499--43511
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[628] [629] [630] [631] [632]
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 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[633] [634] [635] [636] [637] [638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44290--44290
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[639]
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 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[] 
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[][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.append[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 file.copy[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.create[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.exists[][][]\T1/ptm/m/n/10 ,
[640]
Underfull \hbox (badness 3861) in paragraph at lines 44374--44379
[][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 normalizePath[][][]\T1/ptm/m/n/10
 , [][]\T1/pcr/m/n/10 path.expand[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pipe
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Sys.glob[][][]\T1/ptm/m/n/10 ,
[641]
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 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] 
[642]
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[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
[643] [644] [645]
Underfull \hbox (badness 3668) in paragraph at lines 44739--44741
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[646]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 44845--44845
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44920--44920
 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] 
[648]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 44928--44928
 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
 There were 105 warnings ...[] 
[649]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 45022--45022
 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[] 
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 []\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings
AsFactors = FALSE) {[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 45027--45027
 []    \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa
ctors=stringsAsFactors)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45034--45034
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler:  Date -> Matrix
 - dropping time info {sec,min,hour, isdst}[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 45037--45037
 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] 
[650]
Underfull \hbox (badness 6220) in paragraph at lines 45076--45081
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 45076--45081
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
Underfull \hbox (badness 4229) in paragraph at lines 45097--45102
\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[651]
Underfull \hbox (badness 2818) in paragraph at lines 45193--45199
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor 
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
[652]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[653] [654] [655] [656] [657] [658] [659]
Underfull \hbox (badness 2846) in paragraph at lines 45686--45690
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
[660]
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[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[661]) (./compiler-pkg.tex [662]
Chapter 2.
[663]
Underfull \hbox (badness 2884) in paragraph at lines 106--120
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us
ed to con-trol com-piler op-er-a-tion. There are cur-
Underfull \hbox (badness 10000) in paragraph at lines 106--120
\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[664] [665] [666]) (./datasets-pkg.tex
Chapter 3.
[667] [668] [669] [670] [671]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[672]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
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[674] [675] [676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617
 []           \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[] 
[677]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[678] [679]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 837--840
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[680] [681] [682]
Underfull \hbox (badness 1097) in paragraph at lines 1037--1041
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[683]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[684] [685] [686] [687] [688]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[689] [690]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[691] [692] [693]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1738--1741
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[694]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[695] [696]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[697] [698] [699] [700]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2160--2163
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[701] [702] [703]
Overfull \vbox (4.29591pt too high) has occurred while \output is active
[704] [705] [706] [707] [708]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2725--2728
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[709]
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[710]
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[712] [713] [714] [715]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[716] [717] [718] [719] [720] [721] [722] [723]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[724] [725]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 3759--3762
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[726]
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[727]
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[728]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740]
[741] [742]) (./grDevices-pkg.tex
Chapter 4.
[743] [744] [745] [746]
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[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
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[]\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in
[747] [748]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[749] [750]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[751] [752] [753] [754] [755] [756] [757] [758] [759] [760]
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[761] [762] [763]
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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
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[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[764] [765] [766] [767] [768] [769] [770] [771]
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[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not
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\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[772]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[773] [774]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[775] [776]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[777] [778]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[779] [780]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
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 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE) 
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 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[] 
[782] [783] [784] [785] [786]
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[788] [789] [790] [791]
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 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[792]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[793] [794]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[795] [796]
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 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[] 
[797]
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 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[] 
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 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[] 
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 []    \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab =
 "", main=main)[] 
[798]
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 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 
[799]
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[]\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 ,
[800]
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[]\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we
ll for shad-ing points or lines in up to five groups,
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space 
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[801]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[803] [804] [805] [806] [807]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[808] [809] [810] [811] [812] [813]
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[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /
[814] [815]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[816] [817]
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[818]
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[819]
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), \T1/pcr/m/n/10 "CP1251.enc"
[820]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[821] [822] [823]
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[824] [825]
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\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[826]
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[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[827] [828]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[829]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[830] [831]
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[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[832] [833] [834] [835] [836]
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 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[837] [838] [839] [840] [841] [842]
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 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 
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 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[843] [844] [845] [846]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y
pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[847]
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 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[848]
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[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one 
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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 []    \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[] 
[849]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[850]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[851]
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[852]
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[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[853]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[854] [855]
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\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[856] [857] [858]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[859] [860]) (./graphics-pkg.tex
Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use \T1/pcr/m/n/10 library(help =
[861] [862] [863]
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[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[864] [865] [866] [867]
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 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[868] [869]
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 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[870]
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[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 694--698
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[871] [872]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
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 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[873] [874] [875]
Underfull \hbox (badness 10000) in paragraph at lines 964--968
[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10
 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able.
Overfull \hbox (133.98029pt too wide) in paragraph at lines 981--981
 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 983--983
 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 985--985
 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[876] [877] [878] [879]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269
 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. 
outside hinges"):[] 
[880] [881] [882]
Underfull \hbox (badness 1024) in paragraph at lines 1431--1439
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
Underfull \hbox (badness 3375) in paragraph at lines 1465--1467
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[883] [884]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1536--1536
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1543--1543
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[885] [886] [887] [888] [889]
Underfull \hbox (badness 10000) in paragraph at lines 1846--1852
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1866--1866
 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1878--1878
 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1894--1894
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1903--1903
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[890] [891]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1988--1988
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[892] [893]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2117--2117
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2122--2122
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[894] [895]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296
 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8, 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 2297--2297
 []         \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[] 
[896]
Underfull \hbox (badness 1430) in paragraph at lines 2328--2330
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/pcr/m/n/10 "n
" \T1/ptm/m/n/10 to sup-press and see also
[897]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2409--2409
 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 
Underfull \hbox (badness 1009) in paragraph at lines 2421--2428
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[898]
Underfull \hbox (badness 7273) in paragraph at lines 2503--2507
[][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
[899] [900] [901] [902]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2751--2751
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[903]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2788--2788
 []     \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = 
NULL,[] 
[904] [905]
Underfull \hbox (badness 1226) in paragraph at lines 2913--2917
\T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr
/m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2966--2966
 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] 
[906]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2970--2970
 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
Underfull \hbox (badness 10000) in paragraph at lines 3022--3025
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[907] [908] [909]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3227--3227
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3232--3232
 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[910] [911]
Underfull \hbox (badness 10000) in paragraph at lines 3374--3379
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3374--3379
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3374--3379
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[912] [913] [914]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3560--3560
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3579--3579
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[915]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3583--3583
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[916] [917]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3760--3760
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3761--3761
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[918]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3800--3800
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [919]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3852--3852
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3860--3860
 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3862--3862
 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3870--3870
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[920]
Underfull \hbox (badness 10000) in paragraph at lines 3933--3937
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[921] [922]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4045--4045
 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[923] [924]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4199--4199
 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[] 
[925]
Underfull \hbox (badness 3930) in paragraph at lines 4278--4280
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[926] [927] [928] [929] [930]
Underfull \hbox (badness 1286) in paragraph at lines 4589--4592
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4597--4602
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[931] [932]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4694--4694
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4699--4699
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[933]
Underfull \hbox (badness 1264) in paragraph at lines 4890--4903
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[934] [935]
Underfull \hbox (badness 10000) in paragraph at lines 5027--5033
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[936] [937]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5161
[938 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 5219--5221
[939 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//oma.pdf>]
[940]
Underfull \hbox (badness 10000) in paragraph at lines 5409--5411
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5465--5465
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5466--5466
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
Underfull \vbox (badness 10000) has occurred while \output is active [942]
[943] [944] [945] [946] [947]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5831--5831
 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5832--5832
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
[948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5891 \aliasA{plot}{plot.default}{plot}
                                         [949] [950] [951] [952] [953]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6223--6223
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6229--6229
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[954] [955] [956] [957] [958] [959]
Underfull \hbox (badness 10000) in paragraph at lines 6659--6661
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[960] [961]
Underfull \hbox (badness 1028) in paragraph at lines 6753--6755
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6796--6797
[][] 
[962 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6890--6890
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[963]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6921--6921
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [964]
[965]
Underfull \hbox (badness 10000) in paragraph at lines 7043--7045
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7070--7070
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7076--7076
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[966]
Underfull \hbox (badness 2600) in paragraph at lines 7133--7135
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[967] [968] [969] [970]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7365--7365
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[971] [972] [973] [974] [975] [976]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7752--7752
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7756--7756
 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[977]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7768--7768
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[978] [979] [980] [981] [982]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8117--8117
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8120--8120
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8124--8124
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[983] [984] [985]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8295--8295
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[986] [987]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8400--8400
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
Underfull \hbox (badness 2080) in paragraph at lines 8411--8416
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[988]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[989]
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
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 []     \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est fa�ile: 
R�gles, Libert�, Egalit�, Fraternit�...")[] 
[994]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
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<to be read again> 
                   \relax 
l.8966 \HeaderA{units}{Graphical Units}{units}
                                               [996]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
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 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[999]) (./grid-pkg.tex [1000]
Chapter 6.
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
 to the
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it(1, "inches")))[] 
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, height=0.5,[] 
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), name="B"),[] 
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, height=0.5,[] 
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), name="D")),[] 
[1019]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
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ck"), name="r1")[] 
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), name="r2")[] 
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te"), name="r3")[] 
[1033]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[1034]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1041]
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 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
[1044]
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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
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c("left", "bottom")))[] 
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1057] [1058] [1059]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
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 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
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[1072]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1073]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1074] [1075] [1076]
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it(1, "inches")))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
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[1098]
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[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
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\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1099] [1100] [1101] [1102] [1103]
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 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[] 
[1104]
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[1105]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1106] [1107]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/pcr/m/n/10 depth
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1112]) (./methods-pkg.tex
Chapter 7.
[1113] [1114]
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\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1115] [1116] [1117]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1118] [1119]
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 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 
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 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1120]
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 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 
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 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 
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 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 
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 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 
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 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1139] [1140] [1141]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/pcr/m/n/10 where =
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[]
[][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
[1147]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1148] [1149] [1150]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
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[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
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\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1160]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
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[]
[1161] [1162]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =
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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1163]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
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[]\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/
ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
[1164] [1165] [1166]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1170]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1171] [1172] [1173]
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[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the 
im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 ,
[1174] [1175] [1176]
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[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1181]
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
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[1183]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1184] [1185]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1186] [1187] [1188]
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1189] [1190] [1191] [1192] [1193] [1194]
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[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1195] [1196]
Underfull \hbox (badness 1248) in paragraph at lines 6343--6347
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
Underfull \hbox (badness 1960) in paragraph at lines 6343--6347
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1197]
Underfull \hbox (badness 4647) in paragraph at lines 6498--6500
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1198] [1199]
Underfull \hbox (badness 2875) in paragraph at lines 6647--6656
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten 
a good idea; they will be called by call-ing
[1200]
Underfull \vbox (badness 10000) has occurred while \output is active [1201]
[1202] [1203]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1204]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009
 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1205] [1206]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200
 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204
 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1208]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1209] [1210]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
Underfull \hbox (badness 10000) in paragraph at lines 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1211]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7517--7517
 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[] 
[1212]
Underfull \hbox (badness 1019) in paragraph at lines 7663--7670
\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1224]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1225]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1226] [1227] [1228] [1229]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1230] [1231] [1232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1233] [1234] [1235]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429
 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1236] [1237] [1238] [1239]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737
 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1240]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250]
Underfull \hbox (badness 10000) in paragraph at lines 10556--10558
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
Underfull \hbox (badness 1681) in paragraph at lines 10564--10568
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1251] [1252] [1253]) (./parallel-pkg.tex [1254]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1255]
Underfull \hbox (badness 4242) in paragraph at lines 96--98
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1256] [1257]
Underfull \hbox (badness 1024) in paragraph at lines 213--216
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1258]
Underfull \hbox (badness 1320) in paragraph at lines 300--303
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, 
So-laris and Win-dows.
[1259] [1260]
Underfull \hbox (badness 10000) in paragraph at lines 444--446
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1261] [1262] [1263] [1264] [1265]
Underfull \hbox (badness 1917) in paragraph at lines 778--787
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
Underfull \hbox (badness 1178) in paragraph at lines 778--787
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1266] [1267]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 871--871
 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1268] [1269] [1270]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1062--1062
 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1066--1066
 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1271]
Underfull \hbox (badness 5388) in paragraph at lines 1181--1186
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1272]
Underfull \hbox (badness 10000) in paragraph at lines 1205--1213
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1273] [1274]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1358--1358
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1372--1372
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1275]
Underfull \hbox (badness 1577) in paragraph at lines 1401--1404
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1448--1450
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1276] [1277]) (./splines-pkg.tex [1278]
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1287]
Underfull \hbox (badness 1424) in paragraph at lines 597--599
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
 -1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1288] [1289]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 712--712
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1290] [1291] [1292]) (./stats-pkg.tex
Chapter 10.
[1293]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94
 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1294] [1295] [1296] [1297] [1298]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1299]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1300] [1301] [1302] [1303] [1304] [1305]
Underfull \hbox (badness 1024) in paragraph at lines 882--884
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 1544--1548
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1544--1548
\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1544--1548
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1316]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620
 []          \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm 
= TRUE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1623--1623
 []          \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm 
= TRUE)[] 
[1317] [1318]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1770--1770
 []                 \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[] 
[1319]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1782--1782
 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
 specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
] 
[1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330]
[1331] [1332] [1333]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2800--2800
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1334] [1335] [1336] [1337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3040--3040
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1338] [1339] [1340]
Underfull \hbox (badness 10000) in paragraph at lines 3251--3253
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1341]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3300--3300
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3301--3301
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1342] [1343] [1344] [1345] [1346]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3692--3692
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1347] [1348] [1349] [1350]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3971--3971
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1351] [1352] [1353] [1354] [1355]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4260--4260
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4261--4261
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1356] [1357] [1358] [1359]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4501--4501
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1360] [1361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4676--4676
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1362] [1363]
Underfull \hbox (badness 3989) in paragraph at lines 4770--4777
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1364] [1365] [1366] [1367] [1368]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5155--5155
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5157--5157
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1369] [1370] [1371]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5378--5378
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5396--5396
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1372]
Underfull \hbox (badness 2680) in paragraph at lines 5423--5425
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1373] [1374] [1375]
Underfull \hbox (badness 1436) in paragraph at lines 5606--5611
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5606--5611
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5606--5611
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1376] [1377]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5809--5809
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1378] [1379] [1380]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5976--5976
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1381] [1382] [1383]
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 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1384] [1385]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6269--6269
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1386]
Underfull \hbox (badness 10000) in paragraph at lines 6336--6341
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1387] [1388] [1389]
Underfull \hbox (badness 5954) in paragraph at lines 6532--6534
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1390]
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[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6618--6620
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6621--6626
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
[1391]
Underfull \hbox (badness 7238) in paragraph at lines 6657--6660
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6669--6669
 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str =  "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6692--6692
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6707--6707
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
[1392]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6722--6722
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1393] [1394] [1395]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6967--6967
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1396]
[1397] [1398]
Underfull \vbox (badness 10000) has occurred while \output is active [1399]
[1400] [1401] [1402]
Underfull \hbox (badness 10000) in paragraph at lines 7366--7370
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1403]
Underfull \hbox (badness 6493) in paragraph at lines 7465--7468
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1404] [1405]
Underfull \hbox (badness 10000) in paragraph at lines 7602--7605
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1406] [1407] [1408] [1409] [1410] [1411]
Underfull \hbox (badness 10000) in paragraph at lines 8014--8019
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 1210) in paragraph at lines 8369--8371
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1418] [1419] [1420] [1421] [1422] [1423]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8832--8832
 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 
[1424]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8877--8877
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8880--8880
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1425] [1426]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 9018--9018
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1427] [1428] [1429] [1430] [1431] [1432]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9445--9445
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9446--9446
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1433] [1434] [1435]
Underfull \hbox (badness 7291) in paragraph at lines 9625--9627
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1436] [1437] [1438] [1439] [1440] [1441] [1442]
Underfull \hbox (badness 6944) in paragraph at lines 10103--10109
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1443] [1444] [1445]
Underfull \hbox (badness 3758) in paragraph at lines 10317--10320
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1446] [1447] [1448] [1449]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10561--10561
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10587--10592
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1450]
Underfull \hbox (badness 4132) in paragraph at lines 10626--10630
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
Underfull \hbox (badness 1112) in paragraph at lines 10680--10686
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1451]
Underfull \hbox (badness 10000) in paragraph at lines 10731--10734
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1452] [1453] [1454]
Underfull \hbox (badness 2142) in paragraph at lines 10948--10951
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1455]
Underfull \hbox (badness 1708) in paragraph at lines 11029--11033
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1456]
Underfull \hbox (badness 10000) in paragraph at lines 11071--11077
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11109--11114
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1457] [1458]
Underfull \hbox (badness 2635) in paragraph at lines 11242--11245
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1459] [1460] [1461]
Underfull \hbox (badness 1694) in paragraph at lines 11425--11428
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1462]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11526--11526
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1463]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11559--11559
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
Underfull \hbox (badness 10000) in paragraph at lines 11572--11576
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1464] [1465] [1466] [1467] [1468]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11894--11894
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1469]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11909 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11969--11969
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1470]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11981--11981
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
Underfull \hbox (badness 1062) in paragraph at lines 12034--12039
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12051--12053
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1471] [1472] [1473] [1474]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12305--12305
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12306--12306
 []                 \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[] 
[1475] [1476] [1477] [1478] [1479] [1480]
Underfull \hbox (badness 10000) in paragraph at lines 12650--12652
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12673--12675
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1481]
Underfull \hbox (badness 2753) in paragraph at lines 12742--12744
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1482] [1483] [1484] [1485]
Underfull \hbox (badness 6910) in paragraph at lines 12980--12982
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of \T1/pcr/m/n/10 ob
Underfull \hbox (badness 2894) in paragraph at lines 12986--12990
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12986--12990
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13592--13592
 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[] 
[1495]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13693--13693
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1496]
Underfull \hbox (badness 4518) in paragraph at lines 13737--13742
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1497] [1498] [1499]
Underfull \hbox (badness 10000) in paragraph at lines 13936--13940
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1500] [1501] [1502] [1503] [1504]
Underfull \hbox (badness 1163) in paragraph at lines 14270--14278
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1505]
Underfull \hbox (badness 4518) in paragraph at lines 14390--14395
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14578--14578
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14579--14579
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1509] [1510] [1511] [1512] [1513]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14922--14922
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14923--14923
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1514] [1515]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 15016--15016
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1516] [1517] [1518] [1519] [1520] [1521]
Underfull \hbox (badness 2726) in paragraph at lines 15422--15425
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1522]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15516--15516
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16142--16142
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1533] [1534]
Underfull \hbox (badness 1490) in paragraph at lines 16280--16285
\T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are
 re-cy-cled to the num-ber of data frame rows. Un-like
[1535]
Underfull \hbox (badness 1648) in paragraph at lines 16346--16348
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16361--16370
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16361--16370
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1536]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16431--16431
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16432--16432
 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[] 
[1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16989--16989
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1546] [1547] [1548]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17221--17221
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558]
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 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
 
Underfull \vbox (badness 10000) has occurred while \output is active [1560]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17961--17961
 []\T1/pcr/m/n/9 ## Here, requiring close convergence, you need to use more acc
urate numerical[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 17962--17962
 []\T1/pcr/m/n/9 ##  differentiation; this gives Error: "step factor .. reduced
 below \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ..
"[] 
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 []\T1/pcr/m/n/9 try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where
 central diff. work here:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 17966--17966
 []   \T1/pcr/m/n/9 (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral
=TRUE), trace=TRUE))[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17998--17998
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1561] [1562] [1563]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18174--18174
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1564]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18221--18221
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18268--18268
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1565] [1566] [1567] [1568]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 18474--18474
 []             \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[] 
[1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 1248) in paragraph at lines 18789--18792
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 18802--18806
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
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\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1574]
Underfull \hbox (badness 2042) in paragraph at lines 18868--18870
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1575]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18974--18974
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
[1576]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19017--19017
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
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 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19038--19038
 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19058--19058
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
[1577]
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 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
Underfull \hbox (badness 2564) in paragraph at lines 19096--19107
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19096--19107
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1578]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19159--19159
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1579] [1580] [1581]
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 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1582] [1583]
Underfull \hbox (badness 1337) in paragraph at lines 19497--19500
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1584] [1585] [1586] [1587] [1588]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19816--19816
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1589] [1590]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19904--19904
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 
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 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19908--19908
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1591]
Underfull \hbox (badness 10000) in paragraph at lines 19954--19960
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 3049) in paragraph at lines 19995--19999
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1592] [1593] [1594] [1595]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20248--20248
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 1194) in paragraph at lines 20258--20261
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1596]
Underfull \hbox (badness 1107) in paragraph at lines 20316--20318
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1597]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20371--20371
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1598]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20378--20378
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 
[1599]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20472--20472
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1600] [1601]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20601--20601
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1602]
Underfull \hbox (badness 7740) in paragraph at lines 20664--20666
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of
[1603]
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 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1604]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20804--20804
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20809--20809
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615]
[1616] [1617]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 21664--21664
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[] 
[1618]
Underfull \hbox (badness 6859) in paragraph at lines 21731--21738
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21742--21748
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629]
[1630]
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 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1631] [1632] [1633] [1634] [1635]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22772--22772
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22773--22773
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1636] [1637] [1638] [1639] [1640]
Underfull \hbox (badness 1337) in paragraph at lines 23099--23105
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1641] [1642] [1643] [1644] [1645] [1646] [1647]
Underfull \hbox (badness 2913) in paragraph at lines 23524--23527
[]\T1/ptm/m/n/10 used only when \T1/pcr/m/n/10 names \T1/ptm/m/n/10 is true: th
e pre-ci-sion to use when for-mat-
Underfull \hbox (badness 1152) in paragraph at lines 23524--23527
\T1/ptm/m/n/10 ting the per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-s
ions up to 4.0.x, this had been set to
[1648]
Underfull \hbox (badness 10000) in paragraph at lines 23658--23660
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 23658--23660
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 23665--23666
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1649] [1650]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 23776--23776
 []       \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[] 
[1651]
Underfull \hbox (badness 1028) in paragraph at lines 23834--23837
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1652] [1653]
Underfull \hbox (badness 10000) in paragraph at lines 23949--23952
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 7944) in paragraph at lines 24004--24006
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1654]
Underfull \hbox (badness 7944) in paragraph at lines 24066--24068
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1655] [1656]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24168--24168
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1657] [1658]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24285--24285
 []\T1/pcr/m/n/10 #         varying = ___,  # list / matrix / vector (use with 
care)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24286--24286
 []\T1/pcr/m/n/10 #         v.names = ___,  # vector of variable names in long 
format[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24287--24287
 []\T1/pcr/m/n/10 #         timevar, times, # name / values of constructed time
 variable[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24288--24288
 []\T1/pcr/m/n/10 #         idvar, ids)     # name / values of constructed id v
ariable[] 
[1659] [1660]
Underfull \hbox (badness 10000) in paragraph at lines 24448--24453
[][][]\T1/pcr/m/n/10 stack[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 aperm[][][]
\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 relist[][][] \T1/ptm/m/n/10 for re-shap-ing
 the re-sult of [][]\T1/pcr/m/n/10 unlist[][][]\T1/ptm/m/n/10 . [][]\T1/pcr/m/n
/10 xtabs[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 24448--24453
[][]\T1/pcr/m/n/10 as.data.frame.table[][][] \T1/ptm/m/n/10 for cre-at-ing con-
tin-gency ta-bles and con-vert-ing them back to
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24459--24459
 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24460--24460
 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[] 
[1661]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24479--24479
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1662]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24583--24583
 []       \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[] 
[1663]
Underfull \hbox (badness 1033) in paragraph at lines 24626--24632
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
Underfull \hbox (badness 10000) in paragraph at lines 24647--24650
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1664]
Underfull \hbox (badness 2134) in paragraph at lines 24716--24720
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24729--24729
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1665]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24758--24758
 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
 used to fail badly (notably for "Turlach"):[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[] 
[1666] [1667] [1668] [1669] [1670] [1671] [1672]
Underfull \hbox (badness 6268) in paragraph at lines 25228--25233
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
SSmicmen[][][]\T1/ptm/m/n/10 ,
[1673]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 25256--25256
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1674] [1675] [1676]
Underfull \hbox (badness 1867) in paragraph at lines 25433--25435
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 25448--25452
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback =
 use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25448--25452
\T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in
 older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25484--25484
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25491--25491
 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[] 
[1677] [1678] [1679]
Underfull \hbox (badness 2495) in paragraph at lines 25674--25683
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1680]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25756--25756
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
[1681]
Underfull \hbox (badness 1412) in paragraph at lines 25763--25765
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1682]
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 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
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 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25878--25878
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1683] [1684] [1685]
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 []    \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[] 
Underfull \hbox (badness 2547) in paragraph at lines 26106--26112
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1686]
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 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
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 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1687]
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\T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow
 \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value
[1688] [1689]
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 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1690] [1691] [1692] [1693] [1694] [1695]
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 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1696] [1697]
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 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 
[1698]
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 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))  
for when x has ties")[] 
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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
[1699]
Underfull \hbox (badness 2922) in paragraph at lines 27011--27016
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
[1700]
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 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 
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 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 
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 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 
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 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1701]
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[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
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 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 
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 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1702]
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 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 
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 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
[1703]
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 []  \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), 
phi[1]), pos=0, las=1)[] 
Overfull \hbox (106.98032pt too wide) in paragraph at lines 27245--27245
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
Underfull \hbox (badness 2922) in paragraph at lines 27281--27287
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
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 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
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 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
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 []        \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[] 
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 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, control = list(scaleOffset=1))[] 
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 []           \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1
e-11, nDcentral=TRUE), trace=TRUE)[] 
[1705] [1706]
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 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1707]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1708]
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 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1709]
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 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
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 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 
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 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
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 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
[1711]
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 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
[1712]
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 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1713]
Underfull \hbox (badness 6493) in paragraph at lines 27852--27857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27880--27880
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
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 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
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 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 
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 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724]
[1725] [1726] [1727]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1728] [1729]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1730] [1731] [1732]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1733]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1734]
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 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1735]
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[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1736] [1737]
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 []\T1/pcr/m/n/9 symnum(ii, cutpoints =  2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[] 
[1738]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1739] [1740] [1741]
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 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
[1742]
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 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
Underfull \hbox (badness 1616) in paragraph at lines 29786--29789
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1743] [1744]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1745]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1746]
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[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30630--30630
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1756] [1757] [1758] [1759] [1760]
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 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30932--30932
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1761] [1762]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 31058--31058
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
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 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
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[1764] [1765]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774]
Underfull \hbox (badness 1337) in paragraph at lines 31813--31817
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i
-tive nu-meric tol-er-ance, used in
[1775] [1776] [1777]
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 []\T1/pcr/m/n/9 wilcox.test( 4:2,      3:1,     paired=TRUE) # Warning:  canno
t compute exact p-value with ties[] 
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 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) 
# same ties as (4:2, 3:1)[] 
[1778] [1779]
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 []      \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
 = getOption("ts.eps"), ...)[] 
[1780]
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 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1781]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1782]
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 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] 
[1783] [1784]) (./stats4-pkg.tex
Chapter 11.
[1785] [1786] [1787]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
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 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[] 
[1789] [1790] [1791] [1792]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.503 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1793] [1794] [1795])
(./tcltk-pkg.tex [1796]
Chapter 12.
[1797] [1798] [1799] [1800]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[] 
[1801] [1802] [1803]
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1805] [1806] [1807] [1808] [1809] [1810]
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 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[] 
[1811] [1812] [1813] [1814] [1815]
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1816]) (./tools-pkg.tex
Chapter 13.
[1817]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1818]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1819]
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 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1820]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1821]
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 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1822] [1823]
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
ub-di-rec-tory
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 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1831] [1832] [1833]
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 []                              \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[] 
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 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[] 
[1834]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1835]
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[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
[1836] [1837]
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
[1838] [1839] [1840] [1841] [1842]
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 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
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\T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m
/n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong"
[1843] [1844] [1845]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.GSC}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1919 \aliasA{GSC}{find\_gs\_cmd}{GSC}
                                       pdfTeX warning (ext4): destination with 
the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1920 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
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[1849]
Underfull \hbox (badness 1142) in paragraph at lines 2188--2194
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
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 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1850]
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 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 
Underfull \hbox (badness 2359) in paragraph at lines 2250--2257
[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
 and site spe-cific com-pi-la-
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\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
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\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m
/n/10 with
[1851]
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\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1852]
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 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
ong", 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
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\T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m
/n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong"
[1853]
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 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 
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 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1854] [1855] [1856] [1857]
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 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1858]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
[1859] [1860] [1861]
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 []\T1/pcr/m/n/10 checkDocFiles   (package, dir, lib.loc = NULL, chkInternal = 
FALSE) 
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 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = 
FALSE)[] 
[1862] [1863] [1864]
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1865] [1866] [1867] [1868] [1869]
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 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1870] [1871] [1872] [1873]
Underfull \hbox (badness 4108) in paragraph at lines 3758--3765
[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
n the loop-back in-ter-face
[1874]
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 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
[1875]
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 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1876] [1877]
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1878]
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 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1879] [1880] [1881]
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 []  \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[] 
[1882] [1883]
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 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
[1884]
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1885] [1886] [1887] [1888]
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 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
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 []               \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
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\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from
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\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
[1889]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\
T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing
 ex-ist-ing
[1890] [1891] [1892]) (./utils-pkg.tex
Chapter 14.
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1893] [1894] [1895] [1896]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1897]
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\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1898]
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[]\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han-
dles, by de-fault pro-duced by
[1899]
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 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 
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 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 
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 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1900] [1901] [1902]
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 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
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 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
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[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1903] [1904]
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\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1905] [1906] [1907]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1908]
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[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10
 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/
ptm/m/n/10 , in-di-cat-
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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
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\T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \
T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally.
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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1909]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1910] [1911]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1912] [1913] [1914] [1915] [1916] [1917] [1918]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1919]
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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1920]
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 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1921]
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[]\T1/pcr/m/n/10 charClass \T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/ptm
/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-
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\T1/ptm/m/n/10 ac-ter classes which also worked in ear-lier ver-sions is to use
 some-thing like
[1922]
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 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", 
"upper", "xdigit")[] 
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 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[] 
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 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
 Unicode 13.)[] 
[1923] [1924] [1925]
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1926]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1927] [1928]
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 []                 \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] 
[1929]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2618--2618
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1931]
Underfull \hbox (badness 1082) in paragraph at lines 2692--2696
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2697 ... the Clipboard in MS Windows}{clipboard}
                                                   [1932]
Underfull \hbox (badness 1163) in paragraph at lines 2728--2730
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1933]
Underfull \hbox (badness 10000) in paragraph at lines 2816--2818
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1934] [1935] [1936] [1937]
Underfull \hbox (badness 10000) in paragraph at lines 3034--3036
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1938] [1939] [1940] [1941]
Underfull \hbox (badness 1762) in paragraph at lines 3328--3331
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1942]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3421--3421
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1943]
Underfull \hbox (badness 2452) in paragraph at lines 3497--3500
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1944] [1945] [1946] [1947] [1948] [1949]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3906--3906
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1950]
Underfull \hbox (badness 10000) in paragraph at lines 3990--3994
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is 
op-tional on Win-dows: use
[1951]
Underfull \hbox (badness 1072) in paragraph at lines 4058--4066
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1952]
Underfull \hbox (badness 1231) in paragraph at lines 4135--4147
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 4149--4154
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = 
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 4149--4154
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
 of
Underfull \hbox (badness 1331) in paragraph at lines 4149--4154
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1953] [1954]
Underfull \hbox (badness 4660) in paragraph at lines 4269--4272
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4293--4295
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1955] [1956] [1957]
Underfull \hbox (badness 1565) in paragraph at lines 4478--4482
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[1958]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4561--4561
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1959]
Underfull \hbox (badness 1931) in paragraph at lines 4596--4603
[]\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat
-ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1960] [1961] [1962] [1963] [1964]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4920--4920
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1965]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4991 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4991 ...mat Unordered and Ordered Lists}{format}
                                                   [1966] [1967] [1968]
[1969] [1970] [1971] [1972] [1973]
Underfull \hbox (badness 1622) in paragraph at lines 5510--5514
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1974] [1975] [1976] [1977] [1978]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 5832--5832
 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 '  \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 5844--5844
 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported 
as tail.matrix()[] 
[1979] [1980]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5977--5977
 []    \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5978--5978
 []    \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops 
"other" attributes ..[] 
[1981] [1982] [1983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6188--6188
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1984]
Underfull \hbox (badness 10000) in paragraph at lines 6272--6274
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1985]
Underfull \hbox (badness 1502) in paragraph at lines 6321--6326
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 6321--6326
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1986] [1987]
Underfull \hbox (badness 10000) in paragraph at lines 6494--6503
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 6494--6503
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1988]
Underfull \hbox (badness 2150) in paragraph at lines 6558--6561
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6574--6577
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search 
database for sub-se-quent use by
[1989] [1990]
Underfull \hbox (badness 3118) in paragraph at lines 6697--6699
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1991] [1992]
Underfull \hbox (badness 5091) in paragraph at lines 6872--6874
[]\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
[1993]
Underfull \hbox (badness 5331) in paragraph at lines 6888--6894
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6888--6894
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6888--6894
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6902--6909
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
Underfull \hbox (badness 1270) in paragraph at lines 6917--6927
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
 the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
[1994]
Underfull \hbox (badness 10000) in paragraph at lines 6960--6963
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be
Underfull \hbox (badness 10000) in paragraph at lines 6960--6963
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
Underfull \hbox (badness 1424) in paragraph at lines 6968--6971
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
[1995]
Underfull \hbox (badness 2376) in paragraph at lines 7039--7046
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7039--7046
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 7039--7046
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 7047--7050
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1996]
Underfull \hbox (badness 1314) in paragraph at lines 7126--7133
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
Underfull \hbox (badness 10000) in paragraph at lines 7173--7176
[]\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing \T1/pcr/m/n/10 available.pac
kages(filters =
Underfull \hbox (badness 1314) in paragraph at lines 7173--7176
\T1/pcr/m/n/10 "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 ,] \T1/ptm/m/n/
10 will show if the pack-age is avail-able for any \T1/phv/m/n/10 R \T1/ptm/m/n
/10 ver-sion (for
Underfull \hbox (badness 10000) in paragraph at lines 7206--7211
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
[1997]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7229--7229
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
Underfull \hbox (badness 5133) in paragraph at lines 7265--7269
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7279--7282
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1998]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7326--7326
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1999] [2000]
Underfull \hbox (badness 4132) in paragraph at lines 7450--7452
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[2001] [2002] [2003]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7617--7617
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[2004] [2005]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7760--7760
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[2006]
Underfull \hbox (badness 10000) in paragraph at lines 7800--7802
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2007] [2008]
Underfull \hbox (badness 10000) in paragraph at lines 7988--7990
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 7993--7995
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class
[2009] [2010] [2011] [2012]
Underfull \hbox (badness 1859) in paragraph at lines 8221--8224
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[2013]
Underfull \hbox (badness 1655) in paragraph at lines 8315--8318
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8326--8326
 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8334--8334
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 
[2014]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8342--8342
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[2015]
Underfull \hbox (badness 1917) in paragraph at lines 8429--8431
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[2016] [2017] [2018] [2019]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8701--8701
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8702--8702
 []            \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8703--8703
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 8731--8733
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr
/m/n/10 character[][][] \T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 8745--8747
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like \T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8753--8758
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
[2021]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8799--8799
 []          \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8800--8800
 []                                   \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] 
[2022] [2023]
Underfull \hbox (badness 10000) in paragraph at lines 8929--8934
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8929--8934
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8929--8934
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8936--8939
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[2024]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9052--9052
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9053--9053
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[2025] [2026] [2027]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9226--9226
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[2028]
Underfull \hbox (badness 1789) in paragraph at lines 9359--9361
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037]
Underfull \hbox (badness 5203) in paragraph at lines 9932--9935
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[2038] [2039]
Underfull \hbox (badness 1394) in paragraph at lines 10158--10165
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
 , try-ing to com-plete
[2040]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10182--10182
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[2041] [2042]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10343--10343
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2043] [2044] [2045]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10524--10524
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[2046]
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 "no.loss"),[] 
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skip,[] 
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 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
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[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
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 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 
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 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
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\T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 .
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\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2052] [2053] [2054]
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 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2055] [2056] [2057] [2058] [2059]
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\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
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 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
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 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
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 []\T1/pcr/m/n/10 4. |     \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[] 
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 []\T1/pcr/m/n/10 5. |       \-base:::doTryCatch(return(expr), name, parentenv,
 handler)[] 
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 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2064]
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[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
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\T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If
 this is set, then it takes prece-dence over
[2065]
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 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] 
[2066]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
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\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
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\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
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\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2068]
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[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style (\T1/pcr/m/
n/10 "etags"\T1/ptm/m/n/10 ) or vi style
[2069]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
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 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2070] [2071] [2072]
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[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2073] [2074]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12577--12577
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
[2075]
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
 the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and
[2076]
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[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
 con-fig-ured the map-ping of font num-bers to fonts, and
[2077] [2078] [2079] [2080]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
 R \T1/ptm/m/n/10 was built un-der. Where
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2081]
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 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 
[2082]
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[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
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 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2083] [2084] [2085]
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2086]
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[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2087] [2088] [2089]
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 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
Underfull \hbox (badness 2012) in paragraph at lines 13592--13597
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][
]\T1/pcr/m/n/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2090]
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[]\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, 
de-ter-min-ing the \T1/pcr/m/n/10 nlines \T1/ptm/m/n/10 ar-gu-ment to
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 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2091]
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 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 
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 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 
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 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
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[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
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\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
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\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2099] [2100]
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[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
[2101] [2102] [2103]
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 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2104] [2105] [2106] [2107] [2108] [2109]
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
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[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 15021--15026
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
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\T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1
/ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2110]
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\T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av
ailable.packages(contriburl =
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\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
 fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
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[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2111]
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 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt") 
[2112] [2113] [2114]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2115]
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 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
 
[2116]
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 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
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 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2117] [2118]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2119]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2120] [2121]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
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[2122]
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[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/pcr/m/n/10 file =
[2123] [2124] [2125]) [2126] [2127] [2128] (./KernSmooth-pkg.tex
Chapter 15.
[2129]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2130] [2131] [2132] [2133] [2134]
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 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2135] [2136] [2137] [2138]) (./MASS-pkg.tex
Chapter 16.
[2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149]
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 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160]
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[2172]
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
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"F"),[] 
[2173] [2174] [2175] [2176]
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[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[2177] [2178] [2179]
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\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2873--2878
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1
/ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\
T1/ptm/m/n/10 ,
[2180] [2181]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2182] [2183] [2184]
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 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2185]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196]
[2197]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2198] [2199] [2200] [2201] [2202] [2203] [2204]
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 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2205] [2206] [2207]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[2219] [2220] [2221]
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 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2222]
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 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2223] [2224]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6146 ...sical N, P, K Factorial Experiment}{npk}
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ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
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                   \relax 
l.6146 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2225] [2226]
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[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2227] [2228] [2229] [2230]
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 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2231]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2232] [2233] [2234] [2235] [2236] [2237]
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 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
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 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2238]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2239]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2240] [2241]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2242] [2243]
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2244]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2245] [2246] [2247] [2248] [2249] [2250]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2251] [2252]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262] [2263]
[2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272]
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2273]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1
/pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1158) in paragraph at lines 9654--9657
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2274]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
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 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285]
[2286] [2287]) (./Matrix-pkg.tex [2288]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2289]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2290]
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2291]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2292] [2293]
Underfull \hbox (badness 5147) in paragraph at lines 496--499
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2294]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 1668) in paragraph at lines 513--518
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2295] [2296]
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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many*  (k x k) matrices:[] 
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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  where each mat_j is a  k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 matrix\TS1/pcr/m/n/9 '[] 
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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) 
matrix of class  \code{"\linkS4class{dgCMatrix}"}.[] 
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 []        \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[] 
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 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 
[2297]
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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 758--762
\T1/pcr/m/n/10 lapack / double / dsytrf . f$[][] \T1/ptm/m/n/10 and [][]$\T1/pc
r/m/n/10 https : / / www . netlib . org / lapack / double /
[2298] [2299]
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[]\T1/ptm/m/n/10 option [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 in-di-c
at-ing if the re-sult should be sparse, i.e., for-
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\T1/ptm/m/n/10 mally in-her-it-ing from \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"
\T1/ptm/m/n/10 . The de-fault, [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , de-
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\T1/ptm/m/n/10 cides from the ``spar-sity'' of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n
/10 code in
[2300]
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[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing \T1/pcr/m/n/10
 cbind2() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 rbind2() \T1/ptm/m/n/10 meth-ods:
[2301]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2302] [2303]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1168 ...- 'Matrix' S4 Generic and Methods}{chol}
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ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
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<to be read again> 
                   \relax 
l.1168 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2304]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2305]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2306]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
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[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2307]
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[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
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 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 
[2308]
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
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\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls 
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
[2309]
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[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
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\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1658 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
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<to be read again> 
                   \relax 
l.1658 ... Row and Column Sums and Means}{colSums}
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icate ignored
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                   \relax 
l.1659 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
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                   \relax 
l.1680 \aliasA{rowMeans}{colSums}{rowMeans}
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                   \relax 
l.1691 \aliasA{rowSums}{colSums}{rowSums}
                                          [2310]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
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\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
 ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
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[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2311] [2312] [2313]
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[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2314] [2315] [2316] [2317]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2318]
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[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2319] [2320] [2321]
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[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 2649--2653
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
 more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2656--2659
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
 su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2322]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2703--2703
 []    \T1/pcr/m/n/10 .trDiagonal(n, x = 1,            uplo = "U", unitri=TRUE,
 kind)[] 
Underfull \hbox (badness 2689) in paragraph at lines 2712--2714
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2716--2721
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2716--2721
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2323]
Underfull \hbox (badness 1097) in paragraph at lines 2739--2742
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2752--2757
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2324]
Underfull \hbox (badness 3646) in paragraph at lines 2991--2994
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 3023--3025
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 3026--3030
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 3035--3041
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2325]
Underfull \hbox (badness 10000) in paragraph at lines 3042--3046
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3052--3056
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2326] [2327]
Underfull \hbox (badness 10000) in paragraph at lines 3236--3238
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3283--3285
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2328]
Underfull \hbox (badness 2469) in paragraph at lines 3403--3406
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2329] [2330]
Underfull \hbox (badness 10000) in paragraph at lines 3568--3572
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3568--3572
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2331]
Underfull \hbox (badness 2285) in paragraph at lines 3618--3621
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2332] [2333]
Underfull \hbox (badness 10000) in paragraph at lines 3765--3770
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3765--3770
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3777--3780
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2334]
Underfull \hbox (badness 10000) in paragraph at lines 3853--3855
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2335] [2336] [2337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4064--4064
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
Underfull \hbox (badness 3635) in paragraph at lines 4132--4136
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
[2338]
Underfull \hbox (badness 10000) in paragraph at lines 4141--4144
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4141--4144
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4146--4150
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2339] [2340]
Underfull \hbox (badness 3158) in paragraph at lines 4329--4333
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2341] [2342] [2343] [2344]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 4563--4563
 []\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe
ll-Boeing/counterx/counterx.html[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 4570--4570
 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB
/Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4574--4574
 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4577--4577
 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
 the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4587--4587
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2345] [2346] [2347] [2348]
Underfull \hbox (badness 10000) in paragraph at lines 4889--4894
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2349]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4970--4970
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4972--4972
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4976--4976
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4983--4983
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2350] [2351]
Underfull \hbox (badness 4120) in paragraph at lines 5127--5130
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
[2352]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5164--5164
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5170--5170
 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,    
    border.col=NA)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5171--5171
 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[] 
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5175--5175
 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5177--5177
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5184--5184
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5187--5187
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2353]
Underfull \hbox (badness 1817) in paragraph at lines 5276--5285
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the
[2354]
Underfull \hbox (badness 10000) in paragraph at lines 5318--5320
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5320--5323
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
Underfull \hbox (badness 1394) in paragraph at lines 5333--5336
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
Underfull \hbox (badness 4765) in paragraph at lines 5351--5354
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2355] [2356] [2357] [2358] [2359]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5669--5669
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
Underfull \hbox (badness 10000) in paragraph at lines 5752--5755
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5763--5763
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2360]
Underfull \hbox (badness 1622) in paragraph at lines 5800--5805
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5800--5805
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2361]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5862--5862
 []          \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5869--5869
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2362] [2363]
Underfull \hbox (badness 1062) in paragraph at lines 5998--6001
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 6027--6030
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2364]
Underfull \hbox (badness 2635) in paragraph at lines 6139--6144
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6139--6144
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
[2365]
Underfull \hbox (badness 10000) in paragraph at lines 6147--6150
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
Underfull \hbox (badness 10000) in paragraph at lines 6257--6267
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6257--6267
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2366]
Underfull \hbox (badness 3179) in paragraph at lines 6339--6342
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2367]
Underfull \hbox (badness 10000) in paragraph at lines 6437--6440
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2368]
Underfull \hbox (badness 10000) in paragraph at lines 6512--6515
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2369]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6528--6528
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
Underfull \hbox (badness 2443) in paragraph at lines 6567--6573
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6567--6573
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6588--6591
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2370]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6658--6658
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2371] [2372]
Underfull \hbox (badness 10000) in paragraph at lines 6799--6802
[]\T1/ptm/m/n/10 vector of all non-zero en-tries of \T1/pcr/m/n/10 x\T1/ptm/m/n
/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when
[2373]
Underfull \hbox (badness 1490) in paragraph at lines 6821--6823
[]\T1/pcr/m/n/10 mat2triplet() \T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/m/
it/10 in-verse \T1/ptm/m/n/10 func-tion of [][]\T1/pcr/m/n/10 spMatrix[][][] \T
1/ptm/m/n/10 and (one case of)
[2374]
Underfull \hbox (badness 5036) in paragraph at lines 6901--6905
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6901--6905
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
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                   \relax 
l.7000 \aliasA{det}{Matrix-class}{det}
                                       [2376]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
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                   \relax 
l.7176 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7284 ...A{crossprod}{matrix-products}{crossprod}
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                   \relax 
l.7383 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
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\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2378]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
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\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
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\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
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\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
 "dgeMatrix")\T1/ptm/m/n/10 , ma-trix
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
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[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
 $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
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[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2382]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2383] [2384]
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 []   \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[] 
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 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2386]
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[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2387]
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[]\T1/ptm/m/n/10 fast sim-
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l.8291 \HeaderA{norm}{Matrix Norms}{norm}
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h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
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                   \relax 
l.8291 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2389]
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 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2390]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2391]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2392]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2393]
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 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
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[2394]
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[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
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 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
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                   \relax 
l.9093 \aliasA{qr}{qr-methods}{qr}
                                   [2399]
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 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed 
X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] 
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 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 
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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
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 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 
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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2401] [2402]
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 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 
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 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol 
= 1e-7)) # all 14[] 
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
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 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
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                   \relax 
l.9419 ... the Reciprocal Condition Number}{rcond}
                                                   [2403] [2404]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2405] [2406] [2407]
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional
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\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
 not
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2410]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
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ve}) has been already used, duplicate ignored
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                   \relax 
l.9998 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2412]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
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\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
 if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2413]
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2414]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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er-ca-ble to)
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\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2415]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
 \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
 be of-
[2416]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2417] [2418]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
[2419]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2420]
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
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 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2421]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 10796--10796
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10822--10822
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 10824--10824
 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10826--10826
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2422]
[2423]
Underfull \hbox (badness 10000) in paragraph at lines 10967--10971
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha
s been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11007 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2424] [2425]
Underfull \hbox (badness 10000) in paragraph at lines 11137--11139
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 11165--11165
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2426]
Underfull \hbox (badness 5036) in paragraph at lines 11193--11195
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 11327--11333
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2427]
Underfull \hbox (badness 10000) in paragraph at lines 11400--11403
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2428]
Underfull \hbox (badness 10000) in paragraph at lines 11418--11423
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 11433--11435
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2429] [2430]
Underfull \hbox (badness 2698) in paragraph at lines 11558--11564
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2431]
Underfull \hbox (badness 10000) in paragraph at lines 11651--11653
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
Underfull \hbox (badness 10000) in paragraph at lines 11669--11674
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11669--11674
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
[2432]
Underfull \hbox (badness 2591) in paragraph at lines 11677--11682
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
Underfull \hbox (badness 2057) in paragraph at lines 11749--11751
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2433] [2434]
Underfull \hbox (badness 6641) in paragraph at lines 11835--11838
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
Underfull \hbox (badness 5133) in paragraph at lines 11875--11879
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 11875--11879
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2435] [2436]
Underfull \hbox (badness 7649) in paragraph at lines 11982--11984
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2437] [2438] [2439]
Underfull \hbox (badness 7362) in paragraph at lines 12183--12185
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12221--12221
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12222--12222
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2440] [2441] [2442]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12364--12364
 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12377--12377
 []   \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/
x))$modulus))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12382--12382
 []   \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/
x))$modulus))[] 
[2443]
Underfull \hbox (badness 6910) in paragraph at lines 12558--12560
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2444]
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref)                removing `\Rpercent' on input line 12605.
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref)                removing `\Rpercent' on input line 12605.
[2445] [2446]) (./boot-pkg.tex
Chapter 18.
[2447] [2448] [2449] [2450] [2451] [2452] [2453]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2454]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2455] [2456] [2457]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2458]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
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[2460]
Underfull \hbox (badness 10000) in paragraph at lines 1068--1072
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
Underfull \hbox (badness 10000) in paragraph at lines 1068--1072
\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply 
\T1/pcr/m/n/10 "all"
[2461]
Underfull \hbox (badness 1496) in paragraph at lines 1084--1093
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1084--1093
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1105--1111
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2462] [2463] [2464] [2465]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2466] [2467] [2468] [2469] [2470]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2471] [2472] [2473]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2475]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2476] [2477] [2478]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2479]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2440--2441
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2480] [2481]
Underfull \hbox (badness 1077) in paragraph at lines 2536--2540
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple
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\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2482] [2483] [2484] [2485] [2486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 
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 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2487] [2488] [2489]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2490]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2491] [2492] [2493]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2494] [2495] [2496] [2497] [2498] [2499] [2500]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2501] [2502]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2503] [2504] [2505]
Underfull \hbox (badness 10000) in paragraph at lines 4190--4192
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2506]
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 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2507] [2508]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2518] [2519] [2520] [2521]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2522]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2531]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2532]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2533] [2534] [2535] [2536]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2537] [2538]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2539] [2540] [2541]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2542] [2543]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2544] [2545] [2546] [2547] [2548] [2549] [2550] [2551]) (./class-pkg.tex
[2552]
Chapter 19.
[2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560] [2561] [2562] [2563]
[2564] [2565] [2566] [2567] [2568]) (./cluster-pkg.tex
Chapter 20.
[2569]
Underfull \hbox (badness 1655) in paragraph at lines 134--143
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
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\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 134--143
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 134--143
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2570] [2571]
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 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
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 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2572] [2573]
Underfull \vbox (badness 10000) has occurred while \output is active [2574]
[2575]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2576] [2577]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2578]
Underfull \hbox (badness 3078) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2579] [2580]
Underfull \hbox (badness 2941) in paragraph at lines 791--794
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
[2581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
Underfull \hbox (badness 10000) in paragraph at lines 881--883
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2582]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2583]
Underfull \hbox (badness 4872) in paragraph at lines 992--994
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 1006--1010
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2584] [2585]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1120--1120
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1137--1137
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2586]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1175--1175
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
Underfull \hbox (badness 4144) in paragraph at lines 1207--1211
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2587]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1283--1283
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1289--1289
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2588] [2589]
Underfull \hbox (badness 10000) in paragraph at lines 1428--1433
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
[2590]
Underfull \hbox (badness 10000) in paragraph at lines 1476--1479
Underfull \hbox (badness 10000) in paragraph at lines 1493--1497
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1517--1517
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1527--1527
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2591]
Underfull \hbox (badness 5741) in paragraph at lines 1567--1570
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2592]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2593] [2594]
Underfull \hbox (badness 1540) in paragraph at lines 1753--1761
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 =
[2595]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1844--1844
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1863--1863
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2596] [2597] [2598] [2599] [2600]
Underfull \hbox (badness 10000) in paragraph at lines 2182--2185
Underfull \hbox (badness 3179) in paragraph at lines 2196--2202
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2601] [2602]
Underfull \hbox (badness 10000) in paragraph at lines 2354--2357
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2603]
Underfull \hbox (badness 1292) in paragraph at lines 2422--2425
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2604]
Underfull \hbox (badness 6675) in paragraph at lines 2431--2433
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2454--2457
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2605] [2606] [2607]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2670--2670
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2608]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2749--2749
 []    \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[] 
[2609] [2610] [2611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2978--2978
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2612] [2613]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3081--3081
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2614] [2615] [2616]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2617]
Underfull \hbox (badness 10000) in paragraph at lines 3345--3348
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2618]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3396--3396
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2619] [2620] [2621]
Underfull \hbox (badness 10000) in paragraph at lines 3581--3584
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
[2622]
Underfull \hbox (badness 10000) in paragraph at lines 3644--3649
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2623]
Underfull \hbox (badness 3884) in paragraph at lines 3706--3711
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3718--3721
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2624] [2625] [2626]
Underfull \hbox (badness 10000) in paragraph at lines 3903--3906
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3934--3937
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2627]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3987--3987
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3998--4000
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2628] [2629] [2630] [2631]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4191--4191
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4193--4193
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2632] [2633]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4336--4336
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4345--4345
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4347--4347
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4350--4350
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4352--4352
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4359--4359
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2634] [2635] [2636] [2637] [2638] [2639] [2640]
Underfull \hbox (badness 10000) in paragraph at lines 4732--4738
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4748--4750
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4761--4761
 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4763--4763
 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 
s medoid indices  == pam(xclara, 3)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4773--4773
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2641]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4777--4777
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2642]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2643]
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[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2644]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2645] [2646] [2647]) (./foreign-pkg.tex [2648]
Chapter 22.
[2649]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
[2650] [2651]
Underfull \hbox (badness 3601) in paragraph at lines 237--245
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2652]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2653] [2654] [2655]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2656]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
Underfull \hbox (badness 6001) in paragraph at lines 505--514
\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,
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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
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\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2657]
Underfull \hbox (badness 10000) in paragraph at lines 550--558
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / docs . microsoft . com / e
n-[]us / windows / win32 / intl /
Underfull \hbox (badness 7613) in paragraph at lines 568--574
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2658]
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 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 
Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624
 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2659]
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 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661
 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2660] [2661]
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2662] [2663]
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 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2664]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
[2665] [2666]
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[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase 
/ format / data _ types .
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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2667] [2668]
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[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2669]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2670]) (./lattice-pkg.tex
Chapter 23.
[2671]
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\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
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\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / 
ms / departments / sia /
[2672] [2673]
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2674]
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 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2675] [2676] [2677] [2678]
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[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2679] [2680] [2681] [2682]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2683]
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[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2684] [2685]
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[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2686] [2687] [2688]
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[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2689]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2690]
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 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2692]
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2693] [2694] [2695] [2696]
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2697]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2698] [2699] [2700]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2701] [2702] [2703] [2704] [2705]
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 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2706] [2707]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2708]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
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\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2925--2927
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from
[2709]
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[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2710]
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 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
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 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 
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 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
[2711]
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2712]
Underfull \hbox (badness 2913) in paragraph at lines 3187--3194
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3187--3194
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2713] [2714] [2715]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3475 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                 [2716]
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2717] [2718] [2719] [2720] [2721]
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 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2722] [2723]
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2724]
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 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
[2725]
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
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\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2726]
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4214--4218
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2727] [2728]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
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\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2729] [2730] [2731] [2732] [2733]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2734] [2735]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2737] [2738]
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[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2739] [2740] [2741] [2742] [2743]
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[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2744]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2745]
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[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2746] [2747]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
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 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
[2748]
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2749]
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\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2750] [2751]
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[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2752]
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[2754]
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2755] [2756]
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[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6321--6326
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2757]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2758] [2759]
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\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2760]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
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[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
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\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
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\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2772]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2773] [2774]
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
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[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to
[2775]
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2776]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2777] [2778] [2779]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
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\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2788] [2789]
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 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
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 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
[2790]
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ipts, ...)[] 
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2791]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2792] [2793]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2794]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2795] [2796]
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2797]
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[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
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\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2798] [2799] [2800] [2801] [2802] [2803] [2804]
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[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2805] [2806] [2807]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9907 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2808] [2809] [2810]
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\T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2811] [2812]) (./mgcv-pkg.tex
Chapter 24.
[2813] [2814]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2815]
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 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2816] [2817] [2818] [2819]
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[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2820]
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 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[] 
[2821] [2822] [2823]
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[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2824] [2825]
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[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2826] [2827]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2828]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2829]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2835]
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 []    \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[] 
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[] 
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 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[] 
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 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
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 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
[2837]
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 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 
[2838]
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 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 
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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2848] [2849] [2850] [2851] [2852] [2853]
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\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2854]
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2855] [2856] [2857]
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\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2858]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2859] [2860]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878]
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[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2879] [2880]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2884] [2885] [2886] [2887] [2888] [2889] [2890]
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 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2891] [2892] [2893]
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 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2894] [2895]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2896]
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[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
[2897] [2898]
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[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2899]
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[2901] [2902] [2903]
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2904] [2905] [2906] [2907] [2908] [2909] [2910]
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2911] [2912]
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 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
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 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 
[2913]
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 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 
[2914] [2915]
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 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2916] [2917] [2918] [2919] [2920]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
[2921]
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2922] [2923] [2924]
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[2926] [2927]
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 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2928] [2929] [2930] [2931]
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[2934] [2935]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944]
Underfull \hbox (badness 1242) in paragraph at lines 7668--7669
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2945] [2946]
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 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2947]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
[2948]
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
[2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956] [2957] [2958] [2959]
[2960] [2961] [2962] [2963] [2964] [2965] [2966]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9057--9060
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 9057--9060
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2968]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
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\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2969] [2970] [2971] [2972]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
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 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 
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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2973] [2974]
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\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2975] [2976]
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[2978]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2979]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para-
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\T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c
luded terms,
[2980] [2981]
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 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
[2982] [2983] [2984]
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 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2987]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2988]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2989] [2990] [2991]
Underfull \hbox (badness 1253) in paragraph at lines 10474--10476
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2992] [2993] [2994] [2995] [2996]
Underfull \hbox (badness 1946) in paragraph at lines 10727--10734
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 10735--10738
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2997]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[] 
[2998]
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[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2999] [3000] [3001] [3002] [3003]
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 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL) 
[3004] [3005] [3006] [3007] [3008] [3009]
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 []  \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
 + (eps/del))[] 
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 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[] 
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[3011]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
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 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE,[] 
[3012]
Underfull \hbox (badness 10000) in paragraph at lines 11656--11660
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[3013] [3014] [3015]
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 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3016]
Underfull \hbox (badness 1803) in paragraph at lines 11928--11932
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 11940--11952
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
[3017]
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\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 11957--11961
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[3018] [3019] [3020]
Underfull \hbox (badness 6876) in paragraph at lines 12152--12158
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
[3021]
Underfull \hbox (badness 10000) in paragraph at lines 12193--12194
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3022] [3023]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3024]
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 []  \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12377--12377
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
[3025]
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 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 
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 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
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 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
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 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[3026]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 12470--12472
\T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or
[3027] [3028]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3029] [3030]
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 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
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 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 
[3031] [3032]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3033] [3034] [3035] [3036] [3037]
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 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[3038]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3039] [3040]
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[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-
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\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 13303--13306
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[3041] [3042]
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 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[3043]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
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\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[3044] [3045] [3046]
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 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 
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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 13775--13776
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 3396) in paragraph at lines 14035--14038
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14080--14082
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3054] [3055] [3056] [3057] [3058] [3059]
Underfull \hbox (badness 10000) in paragraph at lines 14361--14364
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
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\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063] [3064]
Underfull \hbox (badness 2158) in paragraph at lines 14684--14684
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3065] [3066]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14763--14763
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3067] [3068]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14897--14897
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3069] [3070]
Underfull \hbox (badness 4846) in paragraph at lines 15028--15031
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[3071] [3072] [3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080] [3081]
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16231--16231
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3091] [3092] [3093]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 16441--16441
 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1, 
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 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[] 
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 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[] 
[3094]
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[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 16465--16466
\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected
 by \T1/pcr/m/n/10 ar.row
[3095] [3096] [3097] [3098]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16653--16653
 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16654--16654
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16666--16666
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3099] [3100] [3101]) (./nlme-pkg.tex [3102]
Chapter 25.
[3103]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3104]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3105] [3106] [3107] [3108] [3109]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3110] [3111]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611
 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[] 
[3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[3120]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3121] [3122] [3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3128]
Underfull \hbox (badness 3780) in paragraph at lines 1647--1649
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[3129] [3130] [3131] [3132] [3133]
Underfull \hbox (badness 2042) in paragraph at lines 1996--2002
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3134]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3135]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3136] [3137]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3138]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146]
Underfull \hbox (badness 10000) in paragraph at lines 2849--2853
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3147] [3148] [3149] [3150] [3151] [3152pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d
uplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box 
                                                  
l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE)
                                                  ] [3153] [3154] [3155]
[3156] [3157] [3158]
Underfull \hbox (badness 6493) in paragraph at lines 3585--3593
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166] [3167] [3168] [3169]
[3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180]
[3181] [3182]
Underfull \hbox (badness 10000) in paragraph at lines 5165--5169
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3183] [3184] [3185] [3186] [3187] [3188] [3189]
Underfull \hbox (badness 10000) in paragraph at lines 5597--5600
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] [3198]
Underfull \hbox (badness 2799) in paragraph at lines 6103--6109
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3199]
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[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3200]
Underfull \hbox (badness 2057) in paragraph at lines 6248--6259
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3201]
Underfull \hbox (badness 10000) in paragraph at lines 6312--6314
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3202] [3203] [3204] [3205]
Underfull \hbox (badness 7133) in paragraph at lines 6562--6566
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3206]
Underfull \hbox (badness 10000) in paragraph at lines 6661--6667
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6688--6688
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3207]
Underfull \hbox (badness 10000) in paragraph at lines 6726--6728
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3208]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6756--6756
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3209] [3210] [3211]
Underfull \hbox (badness 10000) in paragraph at lines 6999--7006
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3212]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7017--7017
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7022--7022
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7044--7046
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3213] [3214] [3215]
Underfull \hbox (badness 10000) in paragraph at lines 7259--7264
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3216] [3217] [3218]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7419
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7411--7419
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7411--7419
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7434--7437
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3219] [3220] [3221]
Underfull \hbox (badness 3354) in paragraph at lines 7650--7652
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 8162--8179
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8162--8179
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8205--8205
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3230] [3231] [3232] [3233] [3234]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8479--8479
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3235]
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 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8578 \aliasA{sigma}{lmeObject}{sigma}
                                        [3236] [3237] [3238] [3239] [3240]
[3241] [3242] [3243] [3244] [3245] [3246] [3247]
Underfull \hbox (badness 10000) in paragraph at lines 9330--9337
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9341--9341
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3248]
Underfull \hbox (badness 6300) in paragraph at lines 9423--9426
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3249] [3250] [3251] [3252]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3253]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
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[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
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\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3254] [3255] [3256] [3257] [3258] [3259] [3260] [3261]
Underfull \hbox (badness 7291) in paragraph at lines 10220--10222
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3262] [3263] [3264]
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 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3265]
Underfull \hbox (badness 1596) in paragraph at lines 10465--10491
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3266] [3267] [3268]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10641--10641
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3269] [3270]
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 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10803--10808
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3271]
Underfull \hbox (badness 8075) in paragraph at lines 10825--10829
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10844--10846
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10880--10880
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3272] [3273] [3274] [3275]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11136--11136
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11137--11137
 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0;  ("matrix" in older R)[] 
[3276] [3277] [3278] [3279] [3280] [3281]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11527--11527
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3282] [3283] [3284] [3285] [3286] [3287]
Underfull \hbox (badness 6268) in paragraph at lines 11914--11924
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3288] [3289] [3290] [3291]
Underfull \hbox (badness 10000) in paragraph at lines 12175--12181
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 6876) in paragraph at lines 12497--12499
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
 \T1/ptm/m/n/10 will be con-structed from
[3297] [3298]
Underfull \hbox (badness 2452) in paragraph at lines 12653--12660
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3299]
Underfull \hbox (badness 10000) in paragraph at lines 12718--12724
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3300] [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13307--13307
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3309] [3310] [3311] [3312] [3313]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13672--13672
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3314]
Underfull \hbox (badness 10000) in paragraph at lines 13699--13702
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3315]
Underfull \hbox (badness 1838) in paragraph at lines 13742--13749
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13742--13749
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13799--13799
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3316]
Underfull \hbox (badness 10000) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13806--13809
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13834--13837
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13834--13837
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3317]
Underfull \hbox (badness 10000) in paragraph at lines 13914--13917
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3318]
Underfull \hbox (badness 1472) in paragraph at lines 13939--13946
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3319]
Underfull \hbox (badness 10000) in paragraph at lines 14008--14010
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3320] [3321] [3322] [3323]
Underfull \hbox (badness 1215) in paragraph at lines 14288--14290
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3324] [3325] [3326] [3327]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14532--14532
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3328] [3329] [3330] [3331] [3332] [3333] [3334] [3335] [3336]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15185 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15185 ...Extract Random Effects}{random.effects}
                                                   [3337] [3338] [3339]
[3340] [3341] [3342] [3343] [3344] [3345] [3346]
Underfull \hbox (badness 2126) in paragraph at lines 15825--15829
[]\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199
7). Phar-ma-coki-net-
[3347]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15833--15833
 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15852--15852
 []    \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718
4, tol = 1.5e-5),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15853--15853
 []              \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),              
   tol = 7e-7)[] 
[3348]
Underfull \hbox (badness 1009) in paragraph at lines 15883--15892
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3349] [3350]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16030--16030
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3351] [3352] [3353] [3354] [3355]
Underfull \hbox (badness 10000) in paragraph at lines 16365--16371
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3356]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16396--16396
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3357] [3358] [3359] [3360] [3361] [3362] [3363]
Underfull \hbox (badness 1728) in paragraph at lines 16885--16888
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3364] [3365] [3366] [3367] [3368]
Underfull \hbox (badness 1867) in paragraph at lines 17220--17229
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" 
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3369]
Underfull \hbox (badness 10000) in paragraph at lines 17291--17292
[]\T1/pcr/m/n/10 "Constant plus power of variance
Underfull \hbox (badness 10000) in paragraph at lines 17292--17293
[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3370] [3371] [3372] [3373]
Underfull \hbox (badness 10000) in paragraph at lines 17542--17550
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstProp[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varFixed[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]\T1/ptm/m/n/10 ,
[3374] [3375] [3376] [3377]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17814--17814
 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17816--17816
 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[] 
[3378] [3379] [3380] [3381] [3382] [3383]
Underfull \hbox (badness 10000) in paragraph at lines 18252--18262
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18252--18262
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3384]
Underfull \hbox (badness 3579) in paragraph at lines 18290--18295
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3385]
Underfull \hbox (badness 3579) in paragraph at lines 18354--18359
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3386]
Underfull \hbox (badness 3579) in paragraph at lines 18417--18422
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3387]
Underfull \hbox (badness 1577) in paragraph at lines 18478--18480
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
Underfull \hbox (badness 3579) in paragraph at lines 18480--18485
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3388]
Underfull \hbox (badness 3579) in paragraph at lines 18543--18548
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18576--18585
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18576--18585
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3389]
Underfull \hbox (badness 3579) in paragraph at lines 18615--18620
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3390] [3391]
Underfull \hbox (badness 1009) in paragraph at lines 18761--18770
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3392] [3393]
Underfull \hbox (badness 1009) in paragraph at lines 18893--18902
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3394] [3395] [3396] [3397] [3398] [3399] [3400] [3401] [3402]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3403]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3404] [3405] [3406]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3407]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3408] [3409]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3410]) (./rpart-pkg.tex
Chapter 27.
[3411] [3412] [3413] [3414]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3415] [3416] [3417] [3418]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3419] [3420]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3421] [3422]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3423]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3424] [3425] [3426]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3427]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3428]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3429] [3430] [3431] [3432] [3433] [3434]
Underfull \hbox (badness 1565) in paragraph at lines 1745--1748
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3435] [3436]
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 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3437] [3438] [3439]) (./spatial-pkg.tex [3440]
Chapter 28.
[3441] [3442] [3443] [3444] [3445] [3446]
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[3447] [3448] [3449] [3450] [3451] [3452] [3453] [3454] [3455] [3456] [3457]
[3458] [3459]) (./survival-pkg.tex [3460]
Chapter 29.
[3461] [3462]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
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 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
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 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3463] [3464]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as 
long as
[3465] [3466]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.382 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.382 ... Myelogenous Leukemia survival data}{aml}
                                                   [3467]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
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 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3468]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3469] [3470]
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[3471] [3472]
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 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival 
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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3473] [3474]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 935--935
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3475] [3476] [3477]
Underfull \hbox (badness 1097) in paragraph at lines 1106--1108
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3478] [3479]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3480]
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 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter, 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1308 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3481]
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[]\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea
led by
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 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
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 []  \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[] 
[3482] [3483] [3484]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1575--1575
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
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 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE) 
[3485] [3486] [3487] [3488] [3489]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend \T1/pcr/m/n/10 survival:: \T1/pt
m/m/n/10 onto ev-er-thing, in-clud-ing the spe-
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\T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t
ime,status) ~ age +
[3490]
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[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3491]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2649--2649
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
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 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3500] [3501] [3502]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2908--2908
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3503] [3504] [3505]
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[3506] [3507]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3249--3249
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3508]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3284--3284
 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 
Underfull \hbox (badness 1389) in paragraph at lines 3298--3300
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
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 []        \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[] 
[3509] [3510]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3443--3443
 []                 \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3511] [3512]
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 [] [] 
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[3514]
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 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3515] [3516] [3517] [3518] [3519] [3520] [3521]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4095--4095
 []                    \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3522] [3523]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4241--4241
 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4246--4246
 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4250--4250
 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1])  # differences: yhat[2:
4] - yhat[1][] 
[3524]
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[3526] [3527] [3528] [3529] [3530]
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 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3531] [3532] [3533]
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 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3534]
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 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3535]
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 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3536]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3537]
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 []  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[] 
[3538]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3539] [3540]
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 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1
=FALSE, ...) 
[3541] [3542]
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 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
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 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3543] [3544]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3545]
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3546]
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 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
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 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3547] [3548] [3549] [3550] [3551] [3552]
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 []       \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[] 
[3553] [3554] [3555]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
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\T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3556] [3557] [3558] [3559] [3560]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6799--6799
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6800--6800
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[] 
[3561] [3562]
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 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE) 
[3563]
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 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)]  # rem
ove duplicates[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7008 ...ata from a soldering experiment}{solder}
                                                   [3564] [3565]
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 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3566] [3567] [3568] [3569] [3570]
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 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
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 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3571] [3572] [3573] [3574]
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 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3575] [3576] [3577] [3578]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3579] [3580]
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 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)", 
[3581]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3582] [3583]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 8434--8434
 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3584]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3585]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3586] [3587] [3588] [3589]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8876--8876
 []        \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
 ctype,[] 
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3590] [3591] [3592]
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 []        \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[] 
[3593]
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[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
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\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
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\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
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[3595]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3596] [3597] [3598] [3599] [3600]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3601]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # 
use concordance 
[3602] [3603] [3604]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
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/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3605]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
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 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3609]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
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 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3615] [3616] [3617] [3618] [3619] [3620] [3621]
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 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3622] [3623] [3624])
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
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\T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/pcr/m/n/10 (double.base
Underfull \hbox (badness 1394) in paragraph at lines 143--151
\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As
Underfull \hbox (badness 1668) in paragraph at lines 154--161
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5]
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[]\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]("long.double") \T1/
ptm/m/n/10 is true, there are 10 such
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\T1/pcr/m/n/10 *.exponent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 *.min.exp\T1/ptm/m/n/1
0 , and \T1/pcr/m/n/10 *.max.exp\T1/ptm/m/n/10 , com-puted en-tirely anal-o-gou
sly to their
[6] [7]
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8] [9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11]
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 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v
alue = TRUE)[] 
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 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i
gnore.case = TRUE)[] 
[12] [13] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14]
[15] [16]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 922--922
 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 
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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[17] [18] [19] [20] [21] [22] [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [24] [25]
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[26] [27]
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 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[28]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[29] [30]
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[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[31] [32]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
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[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[33] [34] [35] [36]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[37]
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 []  \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo
ne1970.tab"),[] 
[38]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
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[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[39]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[40] [41] [42]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2730--2730
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE), 
[43] [44] [45] [46] [47] [48] [49] [50] [51]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3399--3399
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 
[52]
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 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 
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 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
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 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 
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 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
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 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[53] [54] [55] [56] [57] [58]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[59] [60] [61] [62] [63] [64] [65]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
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\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[66] [67]
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 []             \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[] 
[68]
Underfull \hbox (badness 4595) in paragraph at lines 4542--4545
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[69] [70]
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 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
[71]
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[72] [73]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[74] [75] [76] [77]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[78] [79] [80] [81] [82] [83]
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[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[84] [85] [86] [87] [88] [89] [90] [91] [92]
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[93] [94] [95]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
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 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows  \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] 
[96] [97]
Underfull \hbox (badness 1635) in paragraph at lines 6573--6576
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing
[98]
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[99] [100]
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 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[101]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6836--6838
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
[102] [103]
Underfull \hbox (badness 1997) in paragraph at lines 6972--6977
[]\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1
0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x
zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC
onnection\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 7010--7013
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
Underfull \hbox (badness 2057) in paragraph at lines 7010--7013
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[104] [105] [106]
Underfull \hbox (badness 1406) in paragraph at lines 7192--7198
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
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\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and 
web-pages gen-er-ated by
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\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
Underfull \hbox (badness 2452) in paragraph at lines 7192--7198
\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 7212--7214
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/pcr/m/n/10 descriptio
n = "clipboard" \T1/ptm/m/n/10 in mode \T1/pcr/m/n/10 "r" \T1/ptm/m/n/10 only. 
This
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\T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http
s : / / specifications . freedesktop .
Underfull \hbox (badness 1735) in paragraph at lines 7254--7261
\T1/pcr/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as \
T1/pcr/m/n/10 "X11_secondary"\T1/ptm/m/n/10 . On most sys-
[107] [108]
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Underfull \vbox (badness 10000) has occurred while \output is active [110]
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 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[111]
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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[112] [113] [114]
Underfull \hbox (badness 10000) in paragraph at lines 7795--7797
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[115] [116] [117]
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 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[118] [119] [120] [121]
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 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[122]
Underfull \hbox (badness 10000) in paragraph at lines 8306--8316
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8306--8316
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be
[123]
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[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[124] [125]
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 []                 \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[] 
[126] [127] [128] [129]
Underfull \hbox (badness 1629) in paragraph at lines 8829--8841
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
Underfull \hbox (badness 5578) in paragraph at lines 8829--8841
\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[130] [131] [132] [133] [134] [135]
Underfull \hbox (badness 10000) in paragraph at lines 9278--9282
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[136] [137]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
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 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9397--9397
 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
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 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[138] [139]
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[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[140] [141] [142]
Underfull \hbox (badness 1603) in paragraph at lines 9779--9782
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[143] [144] [145] [146] [147] [148] [149] [150] [151]
Underfull \hbox (badness 1917) in paragraph at lines 10394--10399
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[152]
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 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10450--10450
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[153] [154]
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\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
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[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
[155] [156]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
Underfull \hbox (badness 10000) in paragraph at lines 10769--10774
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
[157]
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 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[158]
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 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] 
[159] [160]
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 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[161] [162] [163]
Underfull \hbox (badness 6396) in paragraph at lines 11218--11226
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 11444--11447
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[167] [168] [169] [170] [171] [172] [173]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11899--11899
 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[] 
[174] [175] [176]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
[177]
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[178] [179]
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment
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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[180] [181]
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192]
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 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[193] [194] [195] [196] [197] [198] [199]
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\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
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\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[200] [201] [202]
Underfull \hbox (badness 2253) in paragraph at lines 14052--14054
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[203] [204]
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[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr
/m/n/10 fsep =
[205] [206]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[207] [208]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14459--14462
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[209]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[210]
Underfull \hbox (badness 10000) in paragraph at lines 14599--14602
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14609--14609
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[211]
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[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class
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 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[212]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14745--14752
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14753--14757
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[213] [214] [215]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14918--14918
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[216] [217] [218]
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 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15155--15155
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[219]
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[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[220]
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[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[221]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[222] [223]
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[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[224]
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[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
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[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[225]
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[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls
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\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this
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[]\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
[226]
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[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
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\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15786--15786
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
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 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you 
want see the effect[] 
[229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240]
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 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[241]
Underfull \hbox (badness 2418) in paragraph at lines 16751--16755
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 6510) in paragraph at lines 16758--16761
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
[242]
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[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[243] [244] [245]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
[246]
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[247] [248] [249] [250]
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 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 17408--17408
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
[252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17464--17464
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[253] [254] [255] [256]
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 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9))) 
[257]
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 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[] 
[258] [259] [260]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18092--18092
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[261] [262] [263] [264]
Underfull \hbox (badness 2285) in paragraph at lines 18426--18428
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
[265]
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 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[266] [267]
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 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
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 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
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 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 
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 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[268] [269]
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 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
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 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] 
[270] [271] [272]
Underfull \hbox (badness 10000) in paragraph at lines 18952--18954
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[273] [274] [275] [276] [277]
Underfull \hbox (badness 10000) in paragraph at lines 19290--19296
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[278] [279] [280]
Underfull \hbox (badness 4699) in paragraph at lines 19535--19538
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[281] [282]
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 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[283] [284] [285]
Underfull \hbox (badness 4739) in paragraph at lines 19798--19800
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[286]
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 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 
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 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[287] [288] [289] [290] [291] [292] [293] [294]
Underfull \hbox (badness 1975) in paragraph at lines 20459--20462
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[295] [296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1077) in paragraph at lines 20857--20862
[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
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[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
[302]
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[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-
Underfull \hbox (badness 10000) in paragraph at lines 20951--20955
\T1/ptm/m/n/10 tory `\T1/pcr/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/pcr
/m/n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (o
r
[303] [304]
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
Underfull \hbox (badness 1221) in paragraph at lines 21105--21112
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-
[305] [306]
Underfull \hbox (badness 10000) in paragraph at lines 21236--21243
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21357--21361
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[309]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
Underfull \hbox (badness 6592) in paragraph at lines 21427--21432
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
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\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21427--21432
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[310] [311]
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[312]
Underfull \hbox (badness 3343) in paragraph at lines 21659--21663
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[313] [314]
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 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
[315]
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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 prob = 0.2))),[] 
[316]
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 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
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 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
[317]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[318]
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[319]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 22098--22098
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[320] [321]
Underfull \hbox (badness 1400) in paragraph at lines 22266--22270
[][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][]
 \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do
uble[][][] \T1/ptm/m/n/10 (class
[322] [323]
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[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. In nu-meric and
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\T1/ptm/m/n/10 com-plex vec-tors, ze-ros are \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/1
0 and non-zero val-ues are \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 . For [][]\T1/pcr/
m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 10000) in paragraph at lines 22436--22444
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
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\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 23093--23093
 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary =  r ), complex(real =  
r , imaginary = NA ),[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 23094--23094
 []        \T1/pcr/m/n/9 complex(real =  r , imaginary = NaN), complex(real = N
aN, imaginary =  r ))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 23097--23097
 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] 
[334] [335]
Underfull \hbox (badness 1655) in paragraph at lines 23221--23225
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[336] [337] [338] [339]
Underfull \hbox (badness 2277) in paragraph at lines 23470--23473
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
 \T1/ptm/m/n/10 are typ-i-cally prefer-able.
[340] [341]
Underfull \hbox (badness 10000) in paragraph at lines 23601--23604
[]\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc
r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.
0,
[342] [343] [344] [345] [346] [347] [348]
Underfull \hbox (badness 1484) in paragraph at lines 24057--24065
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less 
the OS's de-fault has been
Underfull \hbox (badness 1152) in paragraph at lines 24057--24065
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[349]
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 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[350] [351] [352] [353] [354] [355] [356]
Underfull \hbox (badness 1448) in paragraph at lines 24648--24656
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[357] [358]
Underfull \hbox (badness 3849) in paragraph at lines 24763--24768
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[359]
Underfull \hbox (badness 7308) in paragraph at lines 24840--24846
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
Underfull \hbox (badness 10000) in paragraph at lines 24840--24846
\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) 
\T1/ptm/m/n/10 which are also given by
Underfull \hbox (badness 1210) in paragraph at lines 24840--24846
[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 
. If the en-vi-ron-ment is used as a hash
Underfull \hbox (badness 10000) in paragraph at lines 24850--24853
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 24850--24853
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
[360] [361]
Underfull \hbox (badness 10000) in paragraph at lines 25003--25005
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[362] [363] [364]
Underfull \hbox (badness 6188) in paragraph at lines 25225--25228
[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[365] [366] [367]
Underfull \hbox (badness 1521) in paragraph at lines 25410--25424
\T1/ptm/m/n/10 tion \T1/pcr/m/n/10 GetFinalPathNameByHandle \T1/ptm/m/n/10 and 
in case of an er-ror (such as in-suf-fi-cient per-
[368] [369] [370] [371] [372]
Underfull \hbox (badness 2197) in paragraph at lines 25724--25728
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
Underfull \hbox (badness 2846) in paragraph at lines 25738--25742
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-
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\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
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 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 
[373]
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 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[374]
Underfull \hbox (badness 10000) in paragraph at lines 25832--25838
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
Underfull \hbox (badness 1168) in paragraph at lines 25832--25838
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
Underfull \hbox (badness 10000) in paragraph at lines 25845--25847
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
[375]
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 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] 
[376] [377]
Underfull \hbox (badness 8189) in paragraph at lines 26107--26113
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][]
[378] [379] [380]
Underfull \hbox (badness 1694) in paragraph at lines 26332--26335
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[381] [382] [383] [384]
Underfull \hbox (badness 1603) in paragraph at lines 26579--26581
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[385] [386]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 26706--26714
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[387] [388]
Underfull \hbox (badness 3271) in paragraph at lines 26925--26928
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[389] [390] [391]
Underfull \hbox (badness 3138) in paragraph at lines 27231--27237
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 27231--27237
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 2088) in paragraph at lines 27231--27237
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by
[392]
Underfull \hbox (badness 1194) in paragraph at lines 27244--27247
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and
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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Underfull \hbox (badness 1009) in paragraph at lines 27323--27326
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[393]
Underfull \hbox (badness 10000) in paragraph at lines 27339--27342
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27347--27353
\T1/ptm/m/n/10 build), \T1/pcr/m/n/10 "mac.binary" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS
Underfull \hbox (badness 10000) in paragraph at lines 27347--27353
\T1/ptm/m/n/10 builds). (\T1/pcr/m/n/10 "mac.binary.el-capitan"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5091) in paragraph at lines 27347--27353
\T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina
ry.universal" \T1/ptm/m/n/10 are no longer
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[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
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\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
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\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke \T1/pcr/m/n/10 local({r
Underfull \hbox (badness 10000) in paragraph at lines 27362--27369
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[394] [395] [396] [397]
Underfull \vbox (badness 10000) has occurred while \output is active [398]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27710--27710
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 
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[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[399] [400]
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[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
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\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 28152--28158
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Underfull \hbox (badness 2495) in paragraph at lines 28152--28158
[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
 \T1/ptm/m/n/10 which con-cate-nates and
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 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28186--28186
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
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 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
 ' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling :
[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 28203--28203
 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[] 
[405] [406] [407]
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 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow()  # same as nrow(subset(mt
cars, cyl == 4))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28386--28386
 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so 
is not evaluated[] 
[408]
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[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type =
[409] [410] [411] [412] [413] [414]
Underfull \hbox (badness 2005) in paragraph at lines 28836--28840
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/cmtt/m/n/10 `\T1/pc
r/m/n/10 name\TS1/cmtt/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr
/m/n/10 get[][][](name,envir =
[415]
Underfull \hbox (badness 1796) in paragraph at lines 28904--28907
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[416] [417] [418] [419]
Underfull \hbox (badness 10000) in paragraph at lines 29108--29111
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 29803--29803
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[430] [431] [432] [433]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30094--30094
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 
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 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 
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 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
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 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
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 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [434]
[435]
Underfull \hbox (badness 7415) in paragraph at lines 30200--30204
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[436]
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 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[437]
Underfull \hbox (badness 3713) in paragraph at lines 30390--30401
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[438] [439]
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\T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM
 Trans-ac-tions on Mod-el-ing and Com-puter
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\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh
ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
[440] [441]
Underfull \hbox (badness 1533) in paragraph at lines 30652--30655
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[442] [443]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 30797--30797
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[444] [445]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30959--30959
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 
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 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 
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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 
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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30964--30964
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 
[446]
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 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[447] [448] [449] [450]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 31279--31279
 []\T1/pcr/m/n/9 ## Bit representation  [ sign | exponent | mantissa ] of doubl
e prec numbers :[] 
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 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
 # split one double[] 
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 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31292--31292
 []\T1/pcr/m/n/9 d2b  <- function(x) vapply(as.double(x), function(x)          
 numToBits(x) , raw(64L))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [451]
[452]
Underfull \hbox (badness 4048) in paragraph at lines 31387--31392
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:
Underfull \hbox (badness 1824) in paragraph at lines 31387--31392
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2080) in paragraph at lines 31924--31934
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 infoRDS\T1/ptm/m/n/10 , an \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 list with el-e-ments \T1/pcr/m/n/10 version \T1/ptm/m/n/10 (ver
-sion num-ber, cur-rently 2 or 3),
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 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 7558) in paragraph at lines 32477--32481
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 32487--32489
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
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[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / 
pubs . opengroup . org / onlinepubs /
[468]
Underfull \hbox (badness 1975) in paragraph at lines 32501--32505
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 pcre2pattern \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 pcrepattern man \T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m/n/10 ht
tps : / / www .
[469] [470] [471] [472] [473]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32872--32872
 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3)         # length 24, 3 complete 
replications[] 
[474]
Underfull \hbox (badness 10000) in paragraph at lines 32943--32947
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[475] [476] [477]
Underfull \hbox (badness 2302) in paragraph at lines 33169--33174
[]\T1/pcr/m/n/10 signif \T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-me
nt to the spec-i-fied num-ber of sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for \T1/pcr/m/n/10 numeric x\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 signif(x,dig) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 round(x,
dig
[478] [479]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33302--33302
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
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 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[480] [481] [482] [483] [484] [485] [486]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 33746--33746
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[487] [488] [489] [490] [491] [492]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34183--34183
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[493] [494]
Underfull \hbox (badness 1158) in paragraph at lines 34287--34292
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions
[495] [496]
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 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[497] [498] [499]
Underfull \hbox (badness 8151) in paragraph at lines 34732--34735
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 .
[500] [501] [502] [503]
Underfull \hbox (badness 10000) in paragraph at lines 34947--34952
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10
 gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by =
[504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515]
[516] [517] [518]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 35936--35936
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[519] [520] [521]
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 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
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 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[522]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
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[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[523] [524]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36344--36344
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[525] [526] [527] [528] [529]
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 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36700--36700
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[530] [531] [532]
Underfull \hbox (badness 10000) in paragraph at lines 36925--36927
[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
[533] [534] [535]
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 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
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 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[536] [537] [538] [539]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 37420--37420
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[540]
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[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
 saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert 
a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 37511--37521
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
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\T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an 
en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-
ing
[541]
Underfull \hbox (badness 10000) in paragraph at lines 37557--37563
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,
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\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 37572--37579
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
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\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[542] [543] [544]
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[]\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/
m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[545]
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 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[546] [547] [548] [549] [550] [551] [552] [553] [554]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 38446--38446
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[555] [556] [557]
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 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[558]
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 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[559] [560] [561] [562] [563] [564]
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 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 
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 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[565]
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[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
Underfull \hbox (badness 10000) in paragraph at lines 39228--39235
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
[566]
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 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[567] [568] [569] [570] [571]
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 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[572] [573]
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 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[574]
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 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
Underfull \hbox (badness 2293) in paragraph at lines 39825--39831
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 39825--39831
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the \T1/pcr/m/n/10 glob \T1/ptm/m/n/10 sys-tem call.
Underfull \hbox (badness 4792) in paragraph at lines 39844--39849
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 39844--39849
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[575] [576] [577] [578]
Underfull \hbox (badness 10000) in paragraph at lines 40132--40136
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
[579]
Underfull \hbox (badness 1584) in paragraph at lines 40147--40150
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[580] [581]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 40285--40285
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[582]
Overfull \hbox (19.22812pt too wide) in paragraph at lines 40362--40362
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[583] [584]
Underfull \hbox (badness 1082) in paragraph at lines 40506--40509
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[585] [586] [587]
Underfull \hbox (badness 1038) in paragraph at lines 40697--40700
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[588] [589] [590] [591] [592]
Underfull \hbox (badness 1442) in paragraph at lines 41061--41065
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout =
 TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout =
[593] [594] [595] [596]
Underfull \hbox (badness 4096) in paragraph at lines 41311--41314
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[597]
Underfull \hbox (badness 7888) in paragraph at lines 41425--41429
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
 length(bin) >
[598] [599] [600]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 41579--41579
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (35.4281pt too wide) in paragraph at lines 41581--41581
 []            \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[
] 
Overfull \hbox (55.67578pt too wide) in paragraph at lines 41583--41583
 []                 \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = 
NULL), dim=4, dimnames=list(as.character(2:5)))))[] 
Underfull \hbox (badness 10000) in paragraph at lines 41596--41598
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[601]
Underfull \hbox (badness 10000) in paragraph at lines 41676--41679
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[602] [603]
Underfull \hbox (badness 3872) in paragraph at lines 41794--41797
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[604]
Underfull \hbox (badness 5475) in paragraph at lines 41860--41864
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[605] [606] [607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 42283--42290
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 42339--42348
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 42339--42348
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
[611]
Underfull \hbox (badness 1082) in paragraph at lines 42349--42361
\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 
' in that di-rec-tory states the ver-sion. That op-tion is
Underfull \hbox (badness 1337) in paragraph at lines 42422--42430
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
[612]
Underfull \hbox (badness 10000) in paragraph at lines 42431--42434
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
Underfull \hbox (badness 3460) in paragraph at lines 42485--42488
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 42489--42491
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 42498--42498
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[613] [614] [615]
Underfull \hbox (badness 10000) in paragraph at lines 42719--42721
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[616] [617]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42841--42841
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42843--42843
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
[618] [619]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 42944--42944
 []                                           \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 42946--42946
 []                                           \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[] 
[620] [621] [622]
Underfull \hbox (badness 6542) in paragraph at lines 43220--43222
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[623] [624]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 43339--43339
 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[625]
Underfull \hbox (badness 1708) in paragraph at lines 43407--43415
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 43407--43415
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
[626]
Underfull \hbox (badness 4859) in paragraph at lines 43437--43442
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[627]
Underfull \hbox (badness 3895) in paragraph at lines 43499--43511
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 43499--43511
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[628] [629] [630] [631] [632]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 43821--43821
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[633] [634] [635] [636] [637] [638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44290--44290
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[639]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 44299--44299
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[] 
Underfull \hbox (badness 2057) in paragraph at lines 44365--44371
[][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.append[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 file.copy[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.create[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.exists[][][]\T1/ptm/m/n/10 ,
[640]
Underfull \hbox (badness 3861) in paragraph at lines 44374--44379
[][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 normalizePath[][][]\T1/ptm/m/n/10
 , [][]\T1/pcr/m/n/10 path.expand[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pipe
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Sys.glob[][][]\T1/ptm/m/n/10 ,
[641]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 44467--44467
 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] 
[642]
Underfull \hbox (badness 1803) in paragraph at lines 44520--44523
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 3471) in paragraph at lines 44524--44531
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
[643] [644] [645]
Underfull \hbox (badness 3668) in paragraph at lines 44739--44741
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[646]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 44845--44845
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44920--44920
 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] 
[648]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 44928--44928
 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
 There were 105 warnings ...[] 
[649]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 45022--45022
 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 45026--45026
 []\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings
AsFactors = FALSE) {[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 45027--45027
 []    \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa
ctors=stringsAsFactors)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45034--45034
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler:  Date -> Matrix
 - dropping time info {sec,min,hour, isdst}[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 45037--45037
 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] 
[650]
Underfull \hbox (badness 6220) in paragraph at lines 45076--45081
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
Underfull \hbox (badness 3098) in paragraph at lines 45076--45081
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
Underfull \hbox (badness 10000) in paragraph at lines 45097--45102
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
Underfull \hbox (badness 4229) in paragraph at lines 45097--45102
\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[651]
Underfull \hbox (badness 2818) in paragraph at lines 45193--45199
[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor 
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
[652]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45228--45228
 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[653] [654] [655] [656] [657] [658] [659]
Underfull \hbox (badness 2846) in paragraph at lines 45686--45690
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
Overfull \hbox (4.38043pt too wide) in paragraph at lines 45726--45726
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
[660]
Underfull \hbox (badness 3209) in paragraph at lines 45747--45751
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[661]) (./compiler-pkg.tex [662]
Chapter 2.
[663]
Underfull \hbox (badness 2884) in paragraph at lines 106--120
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us
ed to con-trol com-piler op-er-a-tion. There are cur-
Underfull \hbox (badness 10000) in paragraph at lines 106--120
\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[664] [665] [666]) (./datasets-pkg.tex
Chapter 3.
[667] [668] [669] [670] [671]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[672]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
Underfull \vbox (badness 1472) has occurred while \output is active [673]
[674] [675] [676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617
 []           \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[] 
[677]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 704--707
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[678] [679]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 837--840
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[680] [681] [682]
Underfull \hbox (badness 1097) in paragraph at lines 1037--1041
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[683]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 1152--1155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[684] [685] [686] [687] [688]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[689] [690]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[691] [692] [693]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[694]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[695] [696]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[697] [698] [699] [700]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[701] [702] [703]
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[704] [705] [706] [707] [708]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[709]
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[710]
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[712] [713] [714] [715]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[716] [717] [718] [719] [720] [721] [722] [723]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[724] [725]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[726]
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[727]
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[728]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740]
[741] [742]) (./grDevices-pkg.tex
Chapter 4.
[743] [744] [745] [746]
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[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
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[]\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in
[747] [748]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[749] [750]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[751] [752] [753] [754] [755] [756] [757] [758] [759] [760]
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[761] [762] [763]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
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[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[764] [765] [766] [767] [768] [769] [770] [771]
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[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1893--1898
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[772]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[773] [774]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[775] [776]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[777] [778]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[779] [780]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
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 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE) 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2646--2646
 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[] 
[782] [783] [784] [785] [786]
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[788] [789] [790] [791]
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 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[792]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[793] [794]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[795] [796]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3567--3567
 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[] 
[797]
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 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[] 
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 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[] 
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 []    \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab =
 "", main=main)[] 
[798]
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 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 
[799]
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[]\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 ,
[800]
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[]\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we
ll for shad-ing points or lines in up to five groups,
Underfull \hbox (badness 10000) in paragraph at lines 3862--3866
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space 
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[801]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[803] [804] [805] [806] [807]
Underfull \hbox (badness 5939) in paragraph at lines 4325--4330
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[808] [809] [810] [811] [812] [813]
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[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /
[814] [815]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[816] [817]
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[818]
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[819]
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), \T1/pcr/m/n/10 "CP1251.enc"
[820]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[821] [822] [823]
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[824] [825]
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\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[826]
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[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[827] [828]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[829]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[830] [831]
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[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[832] [833] [834] [835] [836]
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 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[837] [838] [839] [840] [841] [842]
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 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 
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 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[843] [844] [845] [846]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y
pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[847]
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 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[848]
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[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one 
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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 []    \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[] 
[849]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[850]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[851]
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[852]
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[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[853]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[854] [855]
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\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[856] [857] [858]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[859] [860]) (./graphics-pkg.tex
Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use \T1/pcr/m/n/10 library(help =
[861] [862] [863]
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[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[864] [865] [866] [867]
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 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[868] [869]
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 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[870]
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[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
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[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[871] [872]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
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 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[873] [874] [875]
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[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10
 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able.
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 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[] 
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 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 
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 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[876] [877] [878] [879]
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 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. 
outside hinges"):[] 
[880] [881] [882]
Underfull \hbox (badness 1024) in paragraph at lines 1431--1439
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[883] [884]
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 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
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 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
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 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
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 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[885] [886] [887] [888] [889]
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[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1866--1866
 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[] 
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 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[] 
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[890] [891]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[892] [893]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[] 
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 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[894] [895]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296
 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8, 
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 []         \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[] 
[896]
Underfull \hbox (badness 1430) in paragraph at lines 2328--2330
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/pcr/m/n/10 "n
" \T1/ptm/m/n/10 to sup-press and see also
[897]
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 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[898]
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[][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
[899] [900] [901] [902]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[903]
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 []     \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = 
NULL,[] 
[904] [905]
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\T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr
/m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy
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 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] 
[906]
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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[907] [908] [909]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3227--3227
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3232--3232
 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[910] [911]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[912] [913] [914]
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
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 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[915]
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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[916] [917]
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 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[918]
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 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [919]
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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
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 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 
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 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 
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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[920]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[921] [922]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[923] [924]
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 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[] 
[925]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[926] [927] [928] [929] [930]
Underfull \hbox (badness 1286) in paragraph at lines 4589--4592
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4597--4602
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[931] [932]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4694--4694
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 
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 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[933]
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\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[934] [935]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[936] [937]
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[938 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//mai.pdf>]
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[939 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//oma.pdf>]
[940]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[941]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5466--5466
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
Underfull \vbox (badness 10000) has occurred while \output is active [942]
[943] [944] [945] [946] [947]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5831--5831
 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5832--5832
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
[948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5891 \aliasA{plot}{plot.default}{plot}
                                         [949] [950] [951] [952] [953]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6223--6223
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6229--6229
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[954] [955] [956] [957] [958] [959]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[960] [961]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][] 
[962 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//pch.pdf>]
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[963]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[965]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[966]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[967] [968] [969] [970]
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[971] [972] [973] [974] [975] [976]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[977]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[983] [984] [985]
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 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[986] [987]
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 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[988]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[989]
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[990] [991]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[992] [993]
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 []     \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est fa�ile: 
R�gles, Libert�, Egalit�, Fraternit�...")[] 
[994]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8966 \HeaderA{units}{Graphical Units}{units}
                                               [996]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[997] [998]
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 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[999]) (./grid-pkg.tex [1000]
Chapter 6.
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[1009]
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
 to the
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 []                            \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[] 
[1016] [1017] [1018]
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 []               \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[] 
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), name="B"),[] 
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, height=0.5,[] 
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), name="C"),[] 
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, height=0.5,[] 
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), name="D")),[] 
[1019]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1020] [1021] [1022]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[1023] [1024] [1025] [1026] [1027] [1028] [1029]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1030] [1031] [1032]
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1033]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[1034]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[1035] [1036] [1037]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[1038] [1039] [1040]
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1041]
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 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1042] [1043]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
[1044]
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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[1045] [1046] [1047]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1048] [1049] [1050] [1051] [1052]
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1053] [1054]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
c("left", "bottom")))[] 
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1055] [1056]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1057] [1058] [1059]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
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 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
[1072]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1073]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1074] [1075] [1076]
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 []                            \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
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[1098]
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[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
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\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1099] [1100] [1101] [1102] [1103]
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 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[] 
[1104]
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[1105]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1106] [1107]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/pcr/m/n/10 depth
[1108]
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[1110] [1111]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1112]) (./methods-pkg.tex
Chapter 7.
[1113] [1114]
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\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1115] [1116] [1117]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1118] [1119]
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 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 
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 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1120]
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 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 
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 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 
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 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 
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 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 
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 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
] 
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[1134] [1135] [1136]
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1137] [1138]
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1139] [1140] [1141]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/pcr/m/n/10 where =
[1142] [1143]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[]
[][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
[1144] [1145] [1146]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
[1147]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1148] [1149] [1150]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1151] [1152] [1153] [1154] [1155] [1156] [1157]
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[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
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\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1158] [1159]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1160]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
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[]
[1161] [1162]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =
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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1163]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
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[]\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/
ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
[1164] [1165] [1166]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1167] [1168] [1169]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1170]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1171] [1172] [1173]
Underfull \hbox (badness 2126) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the 
im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 ,
[1174] [1175] [1176]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1177] [1178] [1179] [1180]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1181]
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
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[1183]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1184] [1185]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1186] [1187] [1188]
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1189] [1190] [1191] [1192] [1193] [1194]
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[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1195] [1196]
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
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\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1197]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1198] [1199]
Underfull \hbox (badness 2875) in paragraph at lines 6647--6656
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten 
a good idea; they will be called by call-ing
[1200]
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[1202] [1203]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1204]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1205] [1206]
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 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 
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 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1208]
Underfull \hbox (badness 6708) in paragraph at lines 7309--7321
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1209] [1210]
Underfull \hbox (badness 1694) in paragraph at lines 7472--7474
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
Underfull \hbox (badness 10000) in paragraph at lines 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1211]
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 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[] 
[1212]
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\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1224]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1225]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1226] [1227] [1228] [1229]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1230] [1231] [1232]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1233] [1234] [1235]
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 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1236] [1237] [1238] [1239]
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 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1240]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250]
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
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\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1251] [1252] [1253]) (./parallel-pkg.tex [1254]
Chapter 8.
Underfull \hbox (badness 2418) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1255]
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[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1256] [1257]
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[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1258]
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, 
So-laris and Win-dows.
[1259] [1260]
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1261] [1262] [1263] [1264] [1265]
Underfull \hbox (badness 1917) in paragraph at lines 778--787
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
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\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1266] [1267]
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 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1268] [1269] [1270]
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 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1271]
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[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1272]
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[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
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 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1273] [1274]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1358--1358
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1275]
Underfull \hbox (badness 1577) in paragraph at lines 1401--1404
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1448--1450
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1276] [1277]) (./splines-pkg.tex [1278]
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1287]
Underfull \hbox (badness 1424) in paragraph at lines 597--599
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
 -1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1288] [1289]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 712--712
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1290] [1291] [1292]) (./stats-pkg.tex
Chapter 10.
[1293]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91
 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 
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 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1294] [1295] [1296] [1297] [1298]
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 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1299]
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1300] [1301] [1302] [1303] [1304] [1305]
Underfull \hbox (badness 1024) in paragraph at lines 882--884
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 1544--1548
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
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\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1544--1548
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1316]
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 []          \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm 
= TRUE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1623--1623
 []          \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm 
= TRUE)[] 
[1317] [1318]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1770--1770
 []                 \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[] 
[1319]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1782--1782
 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
 specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
] 
[1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330]
[1331] [1332] [1333]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2800--2800
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1334] [1335] [1336] [1337]
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 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1338] [1339] [1340]
Underfull \hbox (badness 10000) in paragraph at lines 3251--3253
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1341]
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 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
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 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1342] [1343] [1344] [1345] [1346]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3692--3692
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1347] [1348] [1349] [1350]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3971--3971
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1351] [1352] [1353] [1354] [1355]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4260--4260
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4261--4261
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1356] [1357] [1358] [1359]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4501--4501
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1360] [1361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4676--4676
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1362] [1363]
Underfull \hbox (badness 3989) in paragraph at lines 4770--4777
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1364] [1365] [1366] [1367] [1368]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5155--5155
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5157--5157
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1369] [1370] [1371]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5378--5378
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5396--5396
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1372]
Underfull \hbox (badness 2680) in paragraph at lines 5423--5425
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1373] [1374] [1375]
Underfull \hbox (badness 1436) in paragraph at lines 5606--5611
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
Underfull \hbox (badness 1377) in paragraph at lines 5606--5611
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5606--5611
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1376] [1377]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5809--5809
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1378] [1379] [1380]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5976--5976
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1381] [1382] [1383]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6161--6161
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1384] [1385]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6269--6269
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1386]
Underfull \hbox (badness 10000) in paragraph at lines 6336--6341
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
[1387] [1388] [1389]
Underfull \hbox (badness 5954) in paragraph at lines 6532--6534
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1390]
Underfull \hbox (badness 2503) in paragraph at lines 6614--6617
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6618--6620
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6621--6626
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
[1391]
Underfull \hbox (badness 7238) in paragraph at lines 6657--6660
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6669--6669
 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str =  "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6692--6692
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6707--6707
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
[1392]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6722--6722
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1393] [1394] [1395]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6967--6967
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1396]
[1397] [1398]
Underfull \vbox (badness 10000) has occurred while \output is active [1399]
[1400] [1401] [1402]
Underfull \hbox (badness 10000) in paragraph at lines 7366--7370
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1403]
Underfull \hbox (badness 6493) in paragraph at lines 7465--7468
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1404] [1405]
Underfull \hbox (badness 10000) in paragraph at lines 7602--7605
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1406] [1407] [1408] [1409] [1410] [1411]
Underfull \hbox (badness 10000) in paragraph at lines 8014--8019
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 1210) in paragraph at lines 8369--8371
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1418] [1419] [1420] [1421] [1422] [1423]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8832--8832
 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 
[1424]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8877--8877
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8880--8880
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1425] [1426]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 9018--9018
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1427] [1428] [1429] [1430] [1431] [1432]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9445--9445
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9446--9446
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1433] [1434] [1435]
Underfull \hbox (badness 7291) in paragraph at lines 9625--9627
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1436] [1437] [1438] [1439] [1440] [1441] [1442]
Underfull \hbox (badness 6944) in paragraph at lines 10103--10109
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1443] [1444] [1445]
Underfull \hbox (badness 3758) in paragraph at lines 10317--10320
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1446] [1447] [1448] [1449]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10561--10561
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10587--10592
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1450]
Underfull \hbox (badness 4132) in paragraph at lines 10626--10630
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
Underfull \hbox (badness 1112) in paragraph at lines 10680--10686
[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1451]
Underfull \hbox (badness 10000) in paragraph at lines 10731--10734
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1452] [1453] [1454]
Underfull \hbox (badness 2142) in paragraph at lines 10948--10951
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1455]
Underfull \hbox (badness 1708) in paragraph at lines 11029--11033
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1456]
Underfull \hbox (badness 10000) in paragraph at lines 11071--11077
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11109--11114
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1457] [1458]
Underfull \hbox (badness 2635) in paragraph at lines 11242--11245
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1459] [1460] [1461]
Underfull \hbox (badness 1694) in paragraph at lines 11425--11428
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1462]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11526--11526
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1463]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11559--11559
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
Underfull \hbox (badness 10000) in paragraph at lines 11572--11576
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1464] [1465] [1466] [1467] [1468]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11894--11894
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1469]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11909 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11969--11969
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1470]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11981--11981
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
Underfull \hbox (badness 1062) in paragraph at lines 12034--12039
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12051--12053
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1471] [1472] [1473] [1474]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12305--12305
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12306--12306
 []                 \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[] 
[1475] [1476] [1477] [1478] [1479] [1480]
Underfull \hbox (badness 10000) in paragraph at lines 12650--12652
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12673--12675
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1481]
Underfull \hbox (badness 2753) in paragraph at lines 12742--12744
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1482] [1483] [1484] [1485]
Underfull \hbox (badness 6910) in paragraph at lines 12980--12982
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of \T1/pcr/m/n/10 ob
Underfull \hbox (badness 2894) in paragraph at lines 12986--12990
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12986--12990
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13592--13592
 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[] 
[1495]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13693--13693
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1496]
Underfull \hbox (badness 4518) in paragraph at lines 13737--13742
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1497] [1498] [1499]
Underfull \hbox (badness 10000) in paragraph at lines 13936--13940
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1500] [1501] [1502] [1503] [1504]
Underfull \hbox (badness 1163) in paragraph at lines 14270--14278
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1505]
Underfull \hbox (badness 4518) in paragraph at lines 14390--14395
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14578--14578
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14579--14579
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1509] [1510] [1511] [1512] [1513]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14922--14922
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
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 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1514] [1515]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 15016--15016
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1516] [1517] [1518] [1519] [1520] [1521]
Underfull \hbox (badness 2726) in paragraph at lines 15422--15425
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1522]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15516--15516
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16142--16142
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1533] [1534]
Underfull \hbox (badness 1490) in paragraph at lines 16280--16285
\T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are
 re-cy-cled to the num-ber of data frame rows. Un-like
[1535]
Underfull \hbox (badness 1648) in paragraph at lines 16346--16348
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16361--16370
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16361--16370
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1536]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16431--16431
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16432--16432
 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[] 
[1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16989--16989
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1546] [1547] [1548]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17221--17221
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558]
Underfull \vbox (badness 10000) has occurred while \output is active [1559]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 17943--17943
 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
 
Underfull \vbox (badness 10000) has occurred while \output is active [1560]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17961--17961
 []\T1/pcr/m/n/9 ## Here, requiring close convergence, you need to use more acc
urate numerical[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 17962--17962
 []\T1/pcr/m/n/9 ##  differentiation; this gives Error: "step factor .. reduced
 below \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ..
"[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 17965--17965
 []\T1/pcr/m/n/9 try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where
 central diff. work here:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 17966--17966
 []   \T1/pcr/m/n/9 (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral
=TRUE), trace=TRUE))[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17998--17998
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1561] [1562] [1563]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18174--18174
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1564]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18221--18221
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18268--18268
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1565] [1566] [1567] [1568]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 18474--18474
 []             \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[] 
[1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 1248) in paragraph at lines 18789--18792
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 18802--18806
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18810--18814
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1574]
Underfull \hbox (badness 2042) in paragraph at lines 18868--18870
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1575]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18974--18974
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
[1576]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19017--19017
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19035--19035
 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19038--19038
 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19058--19058
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
[1577]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19061--19061
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
Underfull \hbox (badness 2564) in paragraph at lines 19096--19107
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19096--19107
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1578]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19159--19159
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1579] [1580] [1581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19386--19386
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1582] [1583]
Underfull \hbox (badness 1337) in paragraph at lines 19497--19500
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1584] [1585] [1586] [1587] [1588]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19816--19816
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1589] [1590]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19904--19904
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 19906--19906
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19908--19908
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1591]
Underfull \hbox (badness 10000) in paragraph at lines 19954--19960
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 3049) in paragraph at lines 19995--19999
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1592] [1593] [1594] [1595]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20248--20248
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 1194) in paragraph at lines 20258--20261
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1596]
Underfull \hbox (badness 1107) in paragraph at lines 20316--20318
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1597]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20371--20371
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1598]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20378--20378
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 
[1599]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20472--20472
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1600] [1601]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20601--20601
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1602]
Underfull \hbox (badness 7740) in paragraph at lines 20664--20666
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of
[1603]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20712--20712
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1604]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20804--20804
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20809--20809
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615]
[1616] [1617]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 21664--21664
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[] 
[1618]
Underfull \hbox (badness 6859) in paragraph at lines 21731--21738
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21742--21748
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629]
[1630]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22488--22488
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1631] [1632] [1633] [1634] [1635]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22772--22772
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22773--22773
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1636] [1637] [1638] [1639] [1640]
Underfull \hbox (badness 1337) in paragraph at lines 23099--23105
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1641] [1642] [1643] [1644] [1645] [1646] [1647]
Underfull \hbox (badness 2913) in paragraph at lines 23524--23527
[]\T1/ptm/m/n/10 used only when \T1/pcr/m/n/10 names \T1/ptm/m/n/10 is true: th
e pre-ci-sion to use when for-mat-
Underfull \hbox (badness 1152) in paragraph at lines 23524--23527
\T1/ptm/m/n/10 ting the per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-s
ions up to 4.0.x, this had been set to
[1648]
Underfull \hbox (badness 10000) in paragraph at lines 23658--23660
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 23658--23660
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 23665--23666
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1649] [1650]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 23776--23776
 []       \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[] 
[1651]
Underfull \hbox (badness 1028) in paragraph at lines 23834--23837
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1652] [1653]
Underfull \hbox (badness 10000) in paragraph at lines 23949--23952
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 7944) in paragraph at lines 24004--24006
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1654]
Underfull \hbox (badness 7944) in paragraph at lines 24066--24068
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1655] [1656]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24168--24168
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1657] [1658]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24285--24285
 []\T1/pcr/m/n/10 #         varying = ___,  # list / matrix / vector (use with 
care)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24286--24286
 []\T1/pcr/m/n/10 #         v.names = ___,  # vector of variable names in long 
format[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24287--24287
 []\T1/pcr/m/n/10 #         timevar, times, # name / values of constructed time
 variable[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24288--24288
 []\T1/pcr/m/n/10 #         idvar, ids)     # name / values of constructed id v
ariable[] 
[1659] [1660]
Underfull \hbox (badness 10000) in paragraph at lines 24448--24453
[][][]\T1/pcr/m/n/10 stack[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 aperm[][][]
\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 relist[][][] \T1/ptm/m/n/10 for re-shap-ing
 the re-sult of [][]\T1/pcr/m/n/10 unlist[][][]\T1/ptm/m/n/10 . [][]\T1/pcr/m/n
/10 xtabs[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 24448--24453
[][]\T1/pcr/m/n/10 as.data.frame.table[][][] \T1/ptm/m/n/10 for cre-at-ing con-
tin-gency ta-bles and con-vert-ing them back to
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24459--24459
 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24460--24460
 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[] 
[1661]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24479--24479
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1662]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24583--24583
 []       \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[] 
[1663]
Underfull \hbox (badness 1033) in paragraph at lines 24626--24632
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
Underfull \hbox (badness 10000) in paragraph at lines 24647--24650
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1664]
Underfull \hbox (badness 2134) in paragraph at lines 24716--24720
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24729--24729
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1665]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24758--24758
 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
 used to fail badly (notably for "Turlach"):[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[] 
[1666] [1667] [1668] [1669] [1670] [1671] [1672]
Underfull \hbox (badness 6268) in paragraph at lines 25228--25233
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
SSmicmen[][][]\T1/ptm/m/n/10 ,
[1673]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 25256--25256
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1674] [1675] [1676]
Underfull \hbox (badness 1867) in paragraph at lines 25433--25435
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 25448--25452
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback =
 use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25448--25452
\T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in
 older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25484--25484
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25491--25491
 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[] 
[1677] [1678] [1679]
Underfull \hbox (badness 2495) in paragraph at lines 25674--25683
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1680]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25756--25756
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
[1681]
Underfull \hbox (badness 1412) in paragraph at lines 25763--25765
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1682]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25850--25850
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25875--25875
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25878--25878
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1683] [1684] [1685]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26102--26102
 []    \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[] 
Underfull \hbox (badness 2547) in paragraph at lines 26106--26112
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1686]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26152--26152
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26173--26173
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1687]
Underfull \hbox (badness 1019) in paragraph at lines 26235--26240
\T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow
 \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value
[1688] [1689]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26365--26365
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1690] [1691] [1692] [1693] [1694] [1695]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26745--26745
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1696] [1697]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26926--26926
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 
[1698]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 26932--26932
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))  
for when x has ties")[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26941--26941
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26942--26942
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
[1699]
Underfull \hbox (badness 2922) in paragraph at lines 27011--27016
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27048--27048
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
[1700]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27051--27051
 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27060--27060
 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27061--27061
 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27065--27065
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1701]
Underfull \hbox (badness 3240) in paragraph at lines 27119--27122
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27140--27140
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27143--27143
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1702]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27226--27226
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27230--27230
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
[1703]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27240--27240
 []  \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), 
phi[1]), pos=0, las=1)[] 
Overfull \hbox (106.98032pt too wide) in paragraph at lines 27245--27245
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
Underfull \hbox (badness 2922) in paragraph at lines 27281--27287
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27303--27303
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27319--27319
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27335--27335
 []        \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[] 
Overfull \hbox (128.58029pt too wide) in paragraph at lines 27338--27338
 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, control = list(scaleOffset=1))[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 27340--27340
 []           \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1
e-11, nDcentral=TRUE), trace=TRUE)[] 
[1705] [1706]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27452--27452
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1707]
Underfull \hbox (badness 2922) in paragraph at lines 27514--27519
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1708]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27552--27552
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
Underfull \hbox (badness 2922) in paragraph at lines 27601--27606
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1709]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27632--27632
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
Underfull \hbox (badness 2922) in paragraph at lines 27666--27671
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27691--27691
 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27695--27695
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27715--27715
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
[1711]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27725--27725
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 
Underfull \hbox (badness 2922) in paragraph at lines 27760--27765
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27782--27782
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
[1712]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27800--27800
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1713]
Underfull \hbox (badness 6493) in paragraph at lines 27852--27857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27880--27880
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27883--27883
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 27886--27886
 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27889--27889
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724]
[1725] [1726] [1727]
Underfull \hbox (badness 3396) in paragraph at lines 28772--28774
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1728] [1729]
Underfull \hbox (badness 2237) in paragraph at lines 28949--28951
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1730] [1731] [1732]
Underfull \hbox (badness 2591) in paragraph at lines 29113--29115
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1733]
Underfull \hbox (badness 2237) in paragraph at lines 29159--29162
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1734]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 29232--29232
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1735]
Underfull \hbox (badness 3407) in paragraph at lines 29341--29345
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1736] [1737]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 29411--29411
 []\T1/pcr/m/n/9 symnum(ii, cutpoints =  2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[] 
[1738]
Underfull \hbox (badness 1337) in paragraph at lines 29474--29478
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1739] [1740] [1741]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29732--29732
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 
[1742]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29760--29760
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
Underfull \hbox (badness 1616) in paragraph at lines 29786--29789
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1743] [1744]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 29865--29865
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1745]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29942--29942
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1746]
Underfull \hbox (badness 2205) in paragraph at lines 30031--30036
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30630--30630
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30631--30631
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1756] [1757] [1758] [1759] [1760]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 30931--30931
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30932--30932
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1761] [1762]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 31058--31058
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 31067--31067
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1763]
[1764] [1765]
Underfull \hbox (badness 1337) in paragraph at lines 31284--31288
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774]
Underfull \hbox (badness 1337) in paragraph at lines 31813--31817
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
Underfull \hbox (badness 5878) in paragraph at lines 31827--31829
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i
-tive nu-meric tol-er-ance, used in
[1775] [1776] [1777]
Overfull \hbox (117.7803pt too wide) in paragraph at lines 32020--32020
 []\T1/pcr/m/n/9 wilcox.test( 4:2,      3:1,     paired=TRUE) # Warning:  canno
t compute exact p-value with ties[] 
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 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) 
# same ties as (4:2, 3:1)[] 
[1778] [1779]
Overfull \hbox (138.78088pt too wide) in paragraph at lines 32181--32181
 []      \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
 = getOption("ts.eps"), ...)[] 
[1780]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 32265--32265
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1781]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1782]
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 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] 
[1783] [1784]) (./stats4-pkg.tex
Chapter 11.
[1785] [1786] [1787]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
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er to 0 and 1[] 
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                                                   [1793] [1794] [1795])
(./tcltk-pkg.tex [1796]
Chapter 12.
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[] 
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
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 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[] 
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1816]) (./tools-pkg.tex
Chapter 13.
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
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ngle = TRUE, 
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
ub-di-rec-tory
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xz"),[] 
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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
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E, ...)[] 
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E, ...)[] 
[1834]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
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tm/m/n/10 and
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[]\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he
r-it-ing from class
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[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and
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hances"))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
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\T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m
/n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong"
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[1849]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag
e
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ogo.svg}{options: width=100}",[] 
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dth=0.5in}}}"),[] 
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[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
 and site spe-cific com-pi-la-
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\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
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\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m
/n/10 with
[1851]
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\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
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 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
ong", 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
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\T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m
/n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong"
[1853]
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 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 
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 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
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 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
[1859] [1860] [1861]
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FALSE) 
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FALSE)[] 
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
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 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
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[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
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net"))[] 
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a
nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
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ests"))[] 
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1879] [1880] [1881]
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 []  \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[] 
[1882] [1883]
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bugs) 
[1884]
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
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[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1885] [1886] [1887] [1888]
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 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 
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 []               \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
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\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from
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\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
[1889]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\
T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing
 ex-ist-ing
[1890] [1891] [1892]) (./utils-pkg.tex
Chapter 14.
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1893] [1894] [1895] [1896]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
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\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1898]
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[]\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han-
dles, by de-fault pro-duced by
[1899]
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 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 
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 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 
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", "Cancel"))),[] 
[1900] [1901] [1902]
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es"), 
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ist(),[] 
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er())[] 
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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
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er())[] 
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[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1903] [1904]
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\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1905] [1906] [1907]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1908]
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[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10
 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/
ptm/m/n/10 , in-di-cat-
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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1661) in paragraph at lines 1108--1116
\T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \
T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1108--1116
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1909]
Underfull \hbox (badness 10000) in paragraph at lines 1228--1231
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1910] [1911]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1311--1311
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1912] [1913] [1914] [1915] [1916] [1917] [1918]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1813--1813
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1919]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1848--1848
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1920]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1994--1994
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1921]
Underfull \hbox (badness 10000) in paragraph at lines 2063--2068
[]\T1/pcr/m/n/10 charClass \T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/ptm
/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-
Underfull \hbox (badness 10000) in paragraph at lines 2063--2068
\T1/ptm/m/n/10 ac-ter classes which also worked in ear-lier ver-sions is to use
 some-thing like
[1922]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2096--2096
 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", 
"upper", "xdigit")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2098--2098
 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106
 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
 Unicode 13.)[] 
[1923] [1924] [1925]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2254--2254
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1926]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2306--2306
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1927] [1928]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2475--2475
 []                 \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] 
[1929]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2498--2498
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2618--2618
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1931]
Underfull \hbox (badness 1082) in paragraph at lines 2692--2696
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2697 ... the Clipboard in MS Windows}{clipboard}
                                                   [1932]
Underfull \hbox (badness 1163) in paragraph at lines 2728--2730
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1933]
Underfull \hbox (badness 10000) in paragraph at lines 2816--2818
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1934] [1935] [1936] [1937]
Underfull \hbox (badness 10000) in paragraph at lines 3034--3036
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1938] [1939] [1940] [1941]
Underfull \hbox (badness 1762) in paragraph at lines 3328--3331
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1942]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3421--3421
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1943]
Underfull \hbox (badness 2452) in paragraph at lines 3497--3500
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1944] [1945] [1946] [1947] [1948] [1949]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3906--3906
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1950]
Underfull \hbox (badness 10000) in paragraph at lines 3990--3994
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is 
op-tional on Win-dows: use
[1951]
Underfull \hbox (badness 1072) in paragraph at lines 4058--4066
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1952]
Underfull \hbox (badness 1231) in paragraph at lines 4135--4147
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 4149--4154
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = 
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 4149--4154
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
 of
Underfull \hbox (badness 1331) in paragraph at lines 4149--4154
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1953] [1954]
Underfull \hbox (badness 4660) in paragraph at lines 4269--4272
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4293--4295
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1955] [1956] [1957]
Underfull \hbox (badness 1565) in paragraph at lines 4478--4482
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[1958]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4561--4561
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1959]
Underfull \hbox (badness 1931) in paragraph at lines 4596--4603
[]\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat
-ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1960] [1961] [1962] [1963] [1964]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4920--4920
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1965]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4991 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4991 ...mat Unordered and Ordered Lists}{format}
                                                   [1966] [1967] [1968]
[1969] [1970] [1971] [1972] [1973]
Underfull \hbox (badness 1622) in paragraph at lines 5510--5514
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1974] [1975] [1976] [1977] [1978]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 5832--5832
 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 '  \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 5844--5844
 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported 
as tail.matrix()[] 
[1979] [1980]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5977--5977
 []    \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5978--5978
 []    \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops 
"other" attributes ..[] 
[1981] [1982] [1983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6188--6188
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1984]
Underfull \hbox (badness 10000) in paragraph at lines 6272--6274
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1985]
Underfull \hbox (badness 1502) in paragraph at lines 6321--6326
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 6321--6326
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1986] [1987]
Underfull \hbox (badness 10000) in paragraph at lines 6494--6503
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 6494--6503
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1988]
Underfull \hbox (badness 2150) in paragraph at lines 6558--6561
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6574--6577
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search 
database for sub-se-quent use by
[1989] [1990]
Underfull \hbox (badness 3118) in paragraph at lines 6697--6699
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1991] [1992]
Underfull \hbox (badness 5091) in paragraph at lines 6872--6874
[]\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
[1993]
Underfull \hbox (badness 5331) in paragraph at lines 6888--6894
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6888--6894
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6888--6894
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6902--6909
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
Underfull \hbox (badness 1270) in paragraph at lines 6917--6927
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
 the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
[1994]
Underfull \hbox (badness 10000) in paragraph at lines 6960--6963
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be
Underfull \hbox (badness 10000) in paragraph at lines 6960--6963
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
Underfull \hbox (badness 1424) in paragraph at lines 6968--6971
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
[1995]
Underfull \hbox (badness 2376) in paragraph at lines 7039--7046
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7039--7046
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 7039--7046
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 7047--7050
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1996]
Underfull \hbox (badness 1314) in paragraph at lines 7126--7133
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
Underfull \hbox (badness 10000) in paragraph at lines 7173--7176
[]\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing \T1/pcr/m/n/10 available.pac
kages(filters =
Underfull \hbox (badness 1314) in paragraph at lines 7173--7176
\T1/pcr/m/n/10 "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 ,] \T1/ptm/m/n/
10 will show if the pack-age is avail-able for any \T1/phv/m/n/10 R \T1/ptm/m/n
/10 ver-sion (for
Underfull \hbox (badness 10000) in paragraph at lines 7206--7211
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
[1997]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7229--7229
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
Underfull \hbox (badness 5133) in paragraph at lines 7265--7269
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7279--7282
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1998]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7326--7326
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1999] [2000]
Underfull \hbox (badness 4132) in paragraph at lines 7450--7452
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[2001] [2002] [2003]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7617--7617
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[2004] [2005]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7760--7760
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[2006]
Underfull \hbox (badness 10000) in paragraph at lines 7800--7802
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2007] [2008]
Underfull \hbox (badness 10000) in paragraph at lines 7988--7990
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 7993--7995
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class
[2009] [2010] [2011] [2012]
Underfull \hbox (badness 1859) in paragraph at lines 8221--8224
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[2013]
Underfull \hbox (badness 1655) in paragraph at lines 8315--8318
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8326--8326
 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8334--8334
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 
[2014]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8342--8342
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[2015]
Underfull \hbox (badness 1917) in paragraph at lines 8429--8431
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[2016] [2017] [2018] [2019]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8701--8701
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8702--8702
 []            \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8703--8703
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 8731--8733
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr
/m/n/10 character[][][] \T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 8745--8747
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like \T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8753--8758
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
[2021]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8799--8799
 []          \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[] 
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 []                                   \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] 
[2022] [2023]
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[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
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[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
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\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion
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\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
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 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
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 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[2028]
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[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
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[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[2038] [2039]
Underfull \hbox (badness 1394) in paragraph at lines 10158--10165
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
 , try-ing to com-plete
[2040]
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 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
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 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2043] [2044] [2045]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10524--10524
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
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 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
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 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
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 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2047]
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[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
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 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 
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 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
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\T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10970--10975
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
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Overfull \hbox (18.78088pt too wide) in paragraph at lines 11203--11203
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2055] [2056] [2057] [2058] [2059]
Underfull \hbox (badness 10000) in paragraph at lines 11464--11468
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11482--11482
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
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 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
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 []\T1/pcr/m/n/10 4. |     \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 11621--11621
 []\T1/pcr/m/n/10 5. |       \-base:::doTryCatch(return(expr), name, parentenv,
 handler)[] 
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 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2064]
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[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
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\T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If
 this is set, then it takes prece-dence over
[2065]
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 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] 
[2066]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
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\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
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\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
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\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2068]
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[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style (\T1/pcr/m/
n/10 "etags"\T1/ptm/m/n/10 ) or vi style
[2069]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12189--12189
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
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[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12401--12407
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 12577--12577
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
[2075]
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
 the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and
[2076]
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[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
 con-fig-ured the map-ping of font num-bers to fonts, and
[2077] [2078] [2079] [2080]
Underfull \hbox (badness 1888) in paragraph at lines 12971--12974
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
 R \T1/ptm/m/n/10 was built un-der. Where
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2081]
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 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 
[2082]
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[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
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 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2083] [2084] [2085]
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
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[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
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 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][
]\T1/pcr/m/n/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13601--13604
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, 
de-ter-min-ing the \T1/pcr/m/n/10 nlines \T1/ptm/m/n/10 ar-gu-ment to
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 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2091]
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 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 
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 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 
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 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
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[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
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\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
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Underfull \hbox (badness 2020) in paragraph at lines 14208--14224
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
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[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
[2101] [2102] [2103]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14518--14518
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2104] [2105] [2106] [2107] [2108] [2109]
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
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[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =
Underfull \hbox (badness 10000) in paragraph at lines 15021--15026
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 15021--15026
\T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1
/ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2110]
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\T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av
ailable.packages(contriburl =
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\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
 fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
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[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2111]
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 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt") 
[2112] [2113] [2114]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
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 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
 
[2116]
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 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
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 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2117] [2118]
Underfull \hbox (badness 1297) in paragraph at lines 15583--15585
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2119]
Underfull \hbox (badness 4036) in paragraph at lines 15630--15632
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2120] [2121]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2122]
Underfull \hbox (badness 1715) in paragraph at lines 15819--15822
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15864--15866
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/pcr/m/n/10 file =
[2123] [2124] [2125]) [2126] [2127] [2128] (./KernSmooth-pkg.tex
Chapter 15.
[2129]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2130] [2131] [2132] [2133] [2134]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2135] [2136] [2137] [2138]) (./MASS-pkg.tex
Chapter 16.
[2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160]
[2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171]
[2172]
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2173] [2174] [2175] [2176]
Underfull \hbox (badness 6559) in paragraph at lines 2703--2706
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[2177] [2178] [2179]
Underfull \hbox (badness 10000) in paragraph at lines 2873--2878
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2873--2878
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1
/ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\
T1/ptm/m/n/10 ,
[2180] [2181]
Underfull \hbox (badness 4686) in paragraph at lines 3041--3043
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2182] [2183] [2184]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3236--3236
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2185]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196]
[2197]
Underfull \hbox (badness 1845) in paragraph at lines 4154--4156
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2198] [2199] [2200] [2201] [2202] [2203] [2204]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4650--4650
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2205] [2206] [2207]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219] [2220] [2221]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5924--5924
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2222]
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 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2223] [2224]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6146 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6146 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2225] [2226]
Underfull \hbox (badness 1783) in paragraph at lines 6266--6270
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2227] [2228] [2229] [2230]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6566--6566
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2231]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2232] [2233] [2234] [2235] [2236] [2237]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7093--7093
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7110--7110
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2238]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
Underfull \hbox (badness 3138) in paragraph at lines 7188--7194
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2239]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2240] [2241]
Underfull \hbox (badness 5091) in paragraph at lines 7367--7370
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2242] [2243]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7497--7497
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2244]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2245] [2246] [2247] [2248] [2249] [2250]
Underfull \hbox (badness 4686) in paragraph at lines 8000--8002
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2251] [2252]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8119--8119
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8143--8147
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262] [2263]
[2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9527--9527
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2273]
Underfull \hbox (badness 2035) in paragraph at lines 9639--9641
[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1
/pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1158) in paragraph at lines 9654--9657
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2274]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9736--9736
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9741--9741
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285]
[2286] [2287]) (./Matrix-pkg.tex [2288]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2289]
Underfull \hbox (badness 1769) in paragraph at lines 95--98
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2290]
Underfull \hbox (badness 2229) in paragraph at lines 159--162
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
Underfull \hbox (badness 1147) in paragraph at lines 159--162
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2291]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2292] [2293]
Underfull \hbox (badness 5147) in paragraph at lines 496--499
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2294]
Underfull \hbox (badness 5119) in paragraph at lines 509--513
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 1668) in paragraph at lines 513--518
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 554--554
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2295] [2296]
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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many*  (k x k) matrices:[] 
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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  where each mat_j is a  k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 matrix\TS1/pcr/m/n/9 '[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 670--670
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) 
matrix of class  \code{"\linkS4class{dgCMatrix}"}.[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 683--683
 []        \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[] 
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 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 
[2297]
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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 758--762
\T1/pcr/m/n/10 lapack / double / dsytrf . f$[][] \T1/ptm/m/n/10 and [][]$\T1/pc
r/m/n/10 https : / / www . netlib . org / lapack / double /
[2298] [2299]
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[]\T1/ptm/m/n/10 option [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 in-di-c
at-ing if the re-sult should be sparse, i.e., for-
Underfull \hbox (badness 7777) in paragraph at lines 877--882
\T1/ptm/m/n/10 mally in-her-it-ing from \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"
\T1/ptm/m/n/10 . The de-fault, [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , de-
Underfull \hbox (badness 6188) in paragraph at lines 877--882
\T1/ptm/m/n/10 cides from the ``spar-sity'' of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n
/10 code in
[2300]
Underfull \hbox (badness 10000) in paragraph at lines 920--925
[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing \T1/pcr/m/n/10
 cbind2() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 rbind2() \T1/ptm/m/n/10 meth-ods:
[2301]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2302] [2303]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1168 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1168 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2304]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2305]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2306]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
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[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2307]
Underfull \hbox (badness 1609) in paragraph at lines 1470--1474
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
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 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 
[2308]
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
Underfull \hbox (badness 10000) in paragraph at lines 1566--1573
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1566--1573
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls 
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
[2309]
Underfull \hbox (badness 1783) in paragraph at lines 1601--1605
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1617--1623
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1658 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1658 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1659 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
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                   \relax 
l.1680 \aliasA{rowMeans}{colSums}{rowMeans}
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ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
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                   \relax 
l.1691 \aliasA{rowSums}{colSums}{rowSums}
                                          [2310]
Underfull \hbox (badness 2922) in paragraph at lines 1745--1749
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 1745--1749
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
 ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1756--1759
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2311] [2312] [2313]
Underfull \hbox (badness 3547) in paragraph at lines 1910--1913
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2314] [2315] [2316] [2317]
Underfull \hbox (badness 1484) in paragraph at lines 2272--2274
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2318]
Underfull \hbox (badness 7379) in paragraph at lines 2368--2370
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2319] [2320] [2321]
Underfull \hbox (badness 4846) in paragraph at lines 2644--2648
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 2649--2653
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
 more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2656--2659
[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
 su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2322]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2703--2703
 []    \T1/pcr/m/n/10 .trDiagonal(n, x = 1,            uplo = "U", unitri=TRUE,
 kind)[] 
Underfull \hbox (badness 2689) in paragraph at lines 2712--2714
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2716--2721
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
Underfull \hbox (badness 3482) in paragraph at lines 2716--2721
[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2323]
Underfull \hbox (badness 1097) in paragraph at lines 2739--2742
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2752--2757
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2324]
Underfull \hbox (badness 3646) in paragraph at lines 2991--2994
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 3023--3025
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
Underfull \hbox (badness 6542) in paragraph at lines 3026--3030
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 3035--3041
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2325]
Underfull \hbox (badness 10000) in paragraph at lines 3042--3046
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3052--3056
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2326] [2327]
Underfull \hbox (badness 10000) in paragraph at lines 3236--3238
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3283--3285
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2328]
Underfull \hbox (badness 2469) in paragraph at lines 3403--3406
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2329] [2330]
Underfull \hbox (badness 10000) in paragraph at lines 3568--3572
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3568--3572
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2331]
Underfull \hbox (badness 2285) in paragraph at lines 3618--3621
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2332] [2333]
Underfull \hbox (badness 10000) in paragraph at lines 3765--3770
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3765--3770
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3777--3780
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2334]
Underfull \hbox (badness 10000) in paragraph at lines 3853--3855
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2335] [2336] [2337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4064--4064
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
Underfull \hbox (badness 3635) in paragraph at lines 4132--4136
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
[2338]
Underfull \hbox (badness 10000) in paragraph at lines 4141--4144
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 4141--4144
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 4146--4150
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2339] [2340]
Underfull \hbox (badness 3158) in paragraph at lines 4329--4333
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2341] [2342] [2343] [2344]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 4563--4563
 []\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe
ll-Boeing/counterx/counterx.html[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 4570--4570
 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB
/Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4574--4574
 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4577--4577
 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
 the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4587--4587
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2345] [2346] [2347] [2348]
Underfull \hbox (badness 10000) in paragraph at lines 4889--4894
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2349]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4970--4970
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4972--4972
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4976--4976
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4983--4983
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2350] [2351]
Underfull \hbox (badness 4120) in paragraph at lines 5127--5130
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
[2352]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5164--5164
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5170--5170
 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,    
    border.col=NA)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 5171--5171
 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[] 
Overfull \hbox (144.78027pt too wide) in paragraph at lines 5175--5175
 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5177--5177
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5184--5184
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
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 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2353]
Underfull \hbox (badness 1817) in paragraph at lines 5276--5285
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the
[2354]
Underfull \hbox (badness 10000) in paragraph at lines 5318--5320
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 5320--5323
[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
Underfull \hbox (badness 1394) in paragraph at lines 5333--5336
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
Underfull \hbox (badness 4765) in paragraph at lines 5351--5354
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2355] [2356] [2357] [2358] [2359]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5669--5669
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
Underfull \hbox (badness 10000) in paragraph at lines 5752--5755
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5763--5763
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2360]
Underfull \hbox (badness 1622) in paragraph at lines 5800--5805
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5800--5805
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2361]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5862--5862
 []          \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5869--5869
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2362] [2363]
Underfull \hbox (badness 1062) in paragraph at lines 5998--6001
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 6027--6030
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2364]
Underfull \hbox (badness 2635) in paragraph at lines 6139--6144
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6139--6144
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
[2365]
Underfull \hbox (badness 10000) in paragraph at lines 6147--6150
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
Underfull \hbox (badness 10000) in paragraph at lines 6257--6267
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6257--6267
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2366]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2367]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2368]
Underfull \hbox (badness 10000) in paragraph at lines 6512--6515
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2369]
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 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6567--6573
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
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[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2370]
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 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2371] [2372]
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[]\T1/ptm/m/n/10 vector of all non-zero en-tries of \T1/pcr/m/n/10 x\T1/ptm/m/n
/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when
[2373]
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[]\T1/pcr/m/n/10 mat2triplet() \T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/m/
it/10 in-verse \T1/ptm/m/n/10 func-tion of [][]\T1/pcr/m/n/10 spMatrix[][][] \T
1/ptm/m/n/10 and (one case of)
[2374]
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[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,
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\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2375]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7000 \aliasA{det}{Matrix-class}{det}
                                       [2376]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2377]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7176 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.7284 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.7383 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
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\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2378]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 7553--7556
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
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\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
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\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
 "dgeMatrix")\T1/ptm/m/n/10 , ma-trix
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2379] [2380]
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[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
 $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
[2381]
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[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2382]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2383] [2384]
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 []   \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[] 
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 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
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[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2386]
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[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2387]
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[]\T1/ptm/m/n/10 fast sim-
[2388]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8291 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.8291 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2389]
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 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2390]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2391]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2392]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2393]
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 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
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[2394]
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[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2395] [2396]
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
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 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2397] [2398]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9093 \aliasA{qr}{qr-methods}{qr}
                                   [2399]
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 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed 
X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] 
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 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 
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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
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 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 
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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2401] [2402]
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 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 
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 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol 
= 1e-7)) # all 14[] 
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
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 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9419 ... the Reciprocal Condition Number}{rcond}
                                                   [2403] [2404]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2405] [2406] [2407]
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional
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\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
 not
[2408] [2409]
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[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2410]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2411]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9998 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2412]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
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\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
 if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2413]
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2414]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
Underfull \hbox (badness 2591) in paragraph at lines 10328--10331
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
Underfull \hbox (badness 2828) in paragraph at lines 10339--10343
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2415]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Underfull \hbox (badness 1158) in paragraph at lines 10375--10381
[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
 \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
 be of-
[2416]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10435--10435
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10436--10436
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2417] [2418]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
[2419]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2420]
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
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 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2421]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
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 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10822--10822
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
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 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10826--10826
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2422]
[2423]
Underfull \hbox (badness 10000) in paragraph at lines 10967--10971
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha
s been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11007 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2424] [2425]
Underfull \hbox (badness 10000) in paragraph at lines 11137--11139
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 11165--11165
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2426]
Underfull \hbox (badness 5036) in paragraph at lines 11193--11195
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 11327--11333
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2427]
Underfull \hbox (badness 10000) in paragraph at lines 11400--11403
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2428]
Underfull \hbox (badness 10000) in paragraph at lines 11418--11423
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 11433--11435
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2429] [2430]
Underfull \hbox (badness 2698) in paragraph at lines 11558--11564
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2431]
Underfull \hbox (badness 10000) in paragraph at lines 11651--11653
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
Underfull \hbox (badness 10000) in paragraph at lines 11669--11674
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11669--11674
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
[2432]
Underfull \hbox (badness 2591) in paragraph at lines 11677--11682
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
Underfull \hbox (badness 2057) in paragraph at lines 11749--11751
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2433] [2434]
Underfull \hbox (badness 6641) in paragraph at lines 11835--11838
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
Underfull \hbox (badness 5133) in paragraph at lines 11875--11879
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 11875--11879
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2435] [2436]
Underfull \hbox (badness 7649) in paragraph at lines 11982--11984
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2437] [2438] [2439]
Underfull \hbox (badness 7362) in paragraph at lines 12183--12185
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12222--12222
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2440] [2441] [2442]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12364--12364
 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
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 []   \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/
x))$modulus))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12382--12382
 []   \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/
x))$modulus))[] 
[2443]
Underfull \hbox (badness 6910) in paragraph at lines 12558--12560
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2444]
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref)                removing `\Rpercent' on input line 12605.
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref)                removing `\Rpercent' on input line 12605.
[2445] [2446]) (./boot-pkg.tex
Chapter 18.
[2447] [2448] [2449] [2450] [2451] [2452] [2453]
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 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2454]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2455] [2456] [2457]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2458]
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 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
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[2460]
Underfull \hbox (badness 10000) in paragraph at lines 1068--1072
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
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\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply 
\T1/pcr/m/n/10 "all"
[2461]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1084--1093
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1105--1111
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2462] [2463] [2464] [2465]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2466] [2467] [2468] [2469] [2470]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2471] [2472] [2473]
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 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2475]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2476] [2477] [2478]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2479]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2440--2441
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2480] [2481]
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[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple
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\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2482] [2483] [2484] [2485] [2486]
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 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 
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 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2487] [2488] [2489]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2490]
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 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2491] [2492] [2493]
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 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2494] [2495] [2496] [2497] [2498] [2499] [2500]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2501] [2502]
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 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2503] [2504] [2505]
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[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2506]
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 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2507] [2508]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2518] [2519] [2520] [2521]
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[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap
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\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2522]
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 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2531]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2532]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2533] [2534] [2535] [2536]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2537] [2538]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2539] [2540] [2541]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2542] [2543]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2544] [2545] [2546] [2547] [2548] [2549] [2550] [2551]) (./class-pkg.tex
[2552]
Chapter 19.
[2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560] [2561] [2562] [2563]
[2564] [2565] [2566] [2567] [2568]) (./cluster-pkg.tex
Chapter 20.
[2569]
Underfull \hbox (badness 1655) in paragraph at lines 134--143
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 134--143
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 134--143
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 134--143
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2570] [2571]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2572] [2573]
Underfull \vbox (badness 10000) has occurred while \output is active [2574]
[2575]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2576] [2577]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2578]
Underfull \hbox (badness 3078) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2579] [2580]
Underfull \hbox (badness 2941) in paragraph at lines 791--794
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
[2581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
Underfull \hbox (badness 10000) in paragraph at lines 881--883
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2582]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2583]
Underfull \hbox (badness 4872) in paragraph at lines 992--994
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 1006--1010
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2584] [2585]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1120--1120
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1137--1137
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2586]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1175--1175
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
Underfull \hbox (badness 4144) in paragraph at lines 1207--1211
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2587]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1283--1283
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1289--1289
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2588] [2589]
Underfull \hbox (badness 10000) in paragraph at lines 1428--1433
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
[2590]
Underfull \hbox (badness 10000) in paragraph at lines 1476--1479
Underfull \hbox (badness 10000) in paragraph at lines 1493--1497
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1517--1517
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1527--1527
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2591]
Underfull \hbox (badness 5741) in paragraph at lines 1567--1570
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2592]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2593] [2594]
Underfull \hbox (badness 1540) in paragraph at lines 1753--1761
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 =
[2595]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1844--1844
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1863--1863
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2596] [2597] [2598] [2599] [2600]
Underfull \hbox (badness 10000) in paragraph at lines 2182--2185
Underfull \hbox (badness 3179) in paragraph at lines 2196--2202
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2601] [2602]
Underfull \hbox (badness 10000) in paragraph at lines 2354--2357
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2603]
Underfull \hbox (badness 1292) in paragraph at lines 2422--2425
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2604]
Underfull \hbox (badness 6675) in paragraph at lines 2431--2433
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2454--2457
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2605] [2606] [2607]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2670--2670
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2608]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2749--2749
 []    \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[] 
[2609] [2610] [2611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2978--2978
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2612] [2613]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3081--3081
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2614] [2615] [2616]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2617]
Underfull \hbox (badness 10000) in paragraph at lines 3345--3348
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2618]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3396--3396
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2619] [2620] [2621]
Underfull \hbox (badness 10000) in paragraph at lines 3581--3584
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
[2622]
Underfull \hbox (badness 10000) in paragraph at lines 3644--3649
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2623]
Underfull \hbox (badness 3884) in paragraph at lines 3706--3711
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3718--3721
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2624] [2625] [2626]
Underfull \hbox (badness 10000) in paragraph at lines 3903--3906
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3934--3937
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2627]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3987--3987
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3998--4000
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2628] [2629] [2630] [2631]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4191--4191
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4193--4193
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2632] [2633]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4336--4336
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4345--4345
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4347--4347
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 
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 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4352--4352
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4359--4359
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2634] [2635] [2636] [2637] [2638] [2639] [2640]
Underfull \hbox (badness 10000) in paragraph at lines 4732--4738
[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4748--4750
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4761--4761
 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4763--4763
 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 
s medoid indices  == pam(xclara, 3)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4773--4773
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2641]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4777--4777
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2642]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2643]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2644]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2645] [2646] [2647]) (./foreign-pkg.tex [2648]
Chapter 22.
[2649]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
[2650] [2651]
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[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2652]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2653] [2654] [2655]
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 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2656]
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 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
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\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,
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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
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\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2657]
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / docs . microsoft . com / e
n-[]us / windows / win32 / intl /
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[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2658]
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 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 
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 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2659]
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 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 
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 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[] 
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 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2660] [2661]
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2662] [2663]
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 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2664]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
[2665] [2666]
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[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase 
/ format / data _ types .
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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2667] [2668]
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[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2669]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2670]) (./lattice-pkg.tex
Chapter 23.
[2671]
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\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
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\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / 
ms / departments / sia /
[2672] [2673]
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2674]
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 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2675] [2676] [2677] [2678]
Underfull \hbox (badness 1221) in paragraph at lines 650--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2679] [2680] [2681] [2682]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2683]
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[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2684] [2685]
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[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2686] [2687] [2688]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2689]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2690]
Underfull \vbox (badness 10000) has occurred while \output is active [2691]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2692]
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2693] [2694] [2695] [2696]
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2697]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2698] [2699] [2700]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2701] [2702] [2703] [2704] [2705]
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 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2706] [2707]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2708]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
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\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
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[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from
[2709]
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[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2710]
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 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
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 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3106--3106
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
[2711]
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2712]
Underfull \hbox (badness 2913) in paragraph at lines 3187--3194
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3187--3194
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2713] [2714] [2715]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3475 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                 [2716]
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2717] [2718] [2719] [2720] [2721]
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 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2722] [2723]
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2724]
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 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
[2725]
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4149--4153
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2726]
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4214--4218
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2727] [2728]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
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\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2729] [2730] [2731] [2732] [2733]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2734] [2735]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2737] [2738]
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[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2739] [2740] [2741] [2742] [2743]
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[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2744]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2745]
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[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2746] [2747]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
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 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
[2748]
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fix),[] 
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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2749]
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\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2750] [2751]
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[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2752]
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[2754]
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2755] [2756]
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[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
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\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2757]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2758] [2759]
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\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2760]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2761] [2762] [2763] [2764] [2765]
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[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
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\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2766] [2767]
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
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\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2768] [2769]
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2770] [2771]
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2772]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2773] [2774]
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
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[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to
[2775]
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2776]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2777] [2778] [2779]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2780] [2781] [2782] [2783] [2784] [2785] [2786] [2787]
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
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\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2788] [2789]
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 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
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 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
[2790]
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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2791]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2792] [2793]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2794]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2795] [2796]
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2797]
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[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
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\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2798] [2799] [2800] [2801] [2802] [2803] [2804]
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[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9676--9680
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2805] [2806] [2807]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9907 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2808] [2809] [2810]
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\T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2811] [2812]) (./mgcv-pkg.tex
Chapter 24.
[2813] [2814]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2815]
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 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2816] [2817] [2818] [2819]
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[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 377--384
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2820]
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 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[] 
[2821] [2822] [2823]
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[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2824] [2825]
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[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2826] [2827]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2828]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2829]
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[2831] [2832] [2833] [2834]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2835]
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 []    \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[] 
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[] 
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 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[] 
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 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
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 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
[2837]
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 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 
[2838]
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 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 
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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2848] [2849] [2850] [2851] [2852] [2853]
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\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2854]
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2855] [2856] [2857]
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\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2858]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2859] [2860]
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[2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878]
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[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2879] [2880]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2891] [2892] [2893]
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 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2896]
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[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
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[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
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[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2899]
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[2901] [2902] [2903]
Underfull \hbox (badness 1577) in paragraph at lines 5369--5372
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5376--5377
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2904] [2905] [2906] [2907] [2908] [2909] [2910]
Underfull \hbox (badness 6708) in paragraph at lines 5765--5766
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2911] [2912]
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 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5839--5839
 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 
[2913]
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 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 
[2914] [2915]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5990--5990
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2916] [2917] [2918] [2919] [2920]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 6327--6327
 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
[2921]
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2922] [2923] [2924]
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[2926] [2927]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 6669--6669
 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2928] [2929] [2930] [2931]
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[2934] [2935]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944]
Underfull \hbox (badness 1242) in paragraph at lines 7668--7669
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2945] [2946]
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 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2947]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
[2948]
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
[2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956] [2957] [2958] [2959]
[2960] [2961] [2962] [2963] [2964] [2965] [2966]
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Underfull \hbox (badness 10000) in paragraph at lines 9057--9060
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9057--9060
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 9057--9060
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2968]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
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\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
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 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 9337--9337
 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2973] [2974]
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\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
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[2978]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2979]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para-
Underfull \hbox (badness 1292) in paragraph at lines 9743--9747
\T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c
luded terms,
[2980] [2981]
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 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
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 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2987]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2988]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2989] [2990] [2991]
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[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2992] [2993] [2994] [2995] [2996]
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[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 10735--10738
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2997]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[] 
[2998]
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[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2999] [3000] [3001] [3002] [3003]
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 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL) 
[3004] [3005] [3006] [3007] [3008] [3009]
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 []  \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
 + (eps/del))[] 
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 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[] 
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[3011]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
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 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE,[] 
[3012]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[3013] [3014] [3015]
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 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3016]
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\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
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\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
[3017]
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\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be
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\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[3018] [3019] [3020]
Underfull \hbox (badness 6876) in paragraph at lines 12152--12158
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
[3021]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3022] [3023]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3024]
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 []  \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[] 
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 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
[3025]
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 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 
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 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
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 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
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 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[3026]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
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\T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or
[3027] [3028]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3029] [3030]
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 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
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 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 
[3031] [3032]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3033] [3034] [3035] [3036] [3037]
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 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[3038]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3039] [3040]
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[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 13303--13306
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 13303--13306
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[3041] [3042]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13387--13387
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[3043]
Underfull \hbox (badness 10000) in paragraph at lines 13432--13438
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 13432--13438
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[3044] [3045] [3046]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13646--13646
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 
Underfull \vbox (badness 10000) has occurred while \output is active [3047]
Underfull \vbox (badness 10000) has occurred while \output is active [3048]
Underfull \hbox (badness 10000) in paragraph at lines 13749--13757
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 13775--13776
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 3396) in paragraph at lines 14035--14038
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14080--14082
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3054] [3055] [3056] [3057] [3058] [3059]
Underfull \hbox (badness 10000) in paragraph at lines 14361--14364
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 14361--14364
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063] [3064]
Underfull \hbox (badness 2158) in paragraph at lines 14684--14684
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3065] [3066]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14763--14763
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3067] [3068]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14897--14897
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3069] [3070]
Underfull \hbox (badness 4846) in paragraph at lines 15028--15031
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[3071] [3072] [3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080] [3081]
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16231--16231
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3091] [3092] [3093]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 16441--16441
 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1, 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 16443--16443
 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16445--16445
 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[] 
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 16465--16466
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 16465--16466
\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected
 by \T1/pcr/m/n/10 ar.row
[3095] [3096] [3097] [3098]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16653--16653
 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16654--16654
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16666--16666
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3099] [3100] [3101]) (./nlme-pkg.tex [3102]
Chapter 25.
[3103]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3104]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3105] [3106] [3107] [3108] [3109]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3110] [3111]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611
 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[] 
[3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[3120]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3121] [3122] [3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3128]
Underfull \hbox (badness 3780) in paragraph at lines 1647--1649
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[3129] [3130] [3131] [3132] [3133]
Underfull \hbox (badness 2042) in paragraph at lines 1996--2002
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3134]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3135]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3136] [3137]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3138]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146]
Underfull \hbox (badness 10000) in paragraph at lines 2849--2853
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3147] [3148] [3149] [3150] [3151] [3152pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d
uplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box 
                                                  
l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE)
                                                  ] [3153] [3154] [3155]
[3156] [3157] [3158]
Underfull \hbox (badness 6493) in paragraph at lines 3585--3593
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166] [3167] [3168] [3169]
[3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180]
[3181] [3182]
Underfull \hbox (badness 10000) in paragraph at lines 5165--5169
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3183] [3184] [3185] [3186] [3187] [3188] [3189]
Underfull \hbox (badness 10000) in paragraph at lines 5597--5600
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] [3198]
Underfull \hbox (badness 2799) in paragraph at lines 6103--6109
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3199]
Underfull \hbox (badness 7133) in paragraph at lines 6164--6168
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3200]
Underfull \hbox (badness 2057) in paragraph at lines 6248--6259
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3201]
Underfull \hbox (badness 10000) in paragraph at lines 6312--6314
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3202] [3203] [3204] [3205]
Underfull \hbox (badness 7133) in paragraph at lines 6562--6566
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3206]
Underfull \hbox (badness 10000) in paragraph at lines 6661--6667
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6688--6688
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3207]
Underfull \hbox (badness 10000) in paragraph at lines 6726--6728
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3208]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6756--6756
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3209] [3210] [3211]
Underfull \hbox (badness 10000) in paragraph at lines 6999--7006
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3212]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7017--7017
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7022--7022
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7044--7046
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3213] [3214] [3215]
Underfull \hbox (badness 10000) in paragraph at lines 7259--7264
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3216] [3217] [3218]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7419
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7411--7419
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7411--7419
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7434--7437
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3219] [3220] [3221]
Underfull \hbox (badness 3354) in paragraph at lines 7650--7652
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 8162--8179
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8162--8179
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8205--8205
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8214--8236
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3230] [3231] [3232] [3233] [3234]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8479--8479
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8527--8529
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3235]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8578 \aliasA{sigma}{lmeObject}{sigma}
                                        [3236] [3237] [3238] [3239] [3240]
[3241] [3242] [3243] [3244] [3245] [3246] [3247]
Underfull \hbox (badness 10000) in paragraph at lines 9330--9337
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9341--9341
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3248]
Underfull \hbox (badness 6300) in paragraph at lines 9423--9426
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3249] [3250] [3251] [3252]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3253]
Underfull \hbox (badness 10000) in paragraph at lines 9712--9715
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9756--9759
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9756--9759
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3254] [3255] [3256] [3257] [3258] [3259] [3260] [3261]
Underfull \hbox (badness 7291) in paragraph at lines 10220--10222
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3262] [3263] [3264]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10436--10436
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3265]
Underfull \hbox (badness 1596) in paragraph at lines 10465--10491
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3266] [3267] [3268]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10641--10641
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3269] [3270]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10792--10792
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10803--10808
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3271]
Underfull \hbox (badness 8075) in paragraph at lines 10825--10829
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10844--10846
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10880--10880
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3272] [3273] [3274] [3275]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11136--11136
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11137--11137
 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0;  ("matrix" in older R)[] 
[3276] [3277] [3278] [3279] [3280] [3281]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11527--11527
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3282] [3283] [3284] [3285] [3286] [3287]
Underfull \hbox (badness 6268) in paragraph at lines 11914--11924
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3288] [3289] [3290] [3291]
Underfull \hbox (badness 10000) in paragraph at lines 12175--12181
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 6876) in paragraph at lines 12497--12499
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
 \T1/ptm/m/n/10 will be con-structed from
[3297] [3298]
Underfull \hbox (badness 2452) in paragraph at lines 12653--12660
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3299]
Underfull \hbox (badness 10000) in paragraph at lines 12718--12724
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3300] [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13307--13307
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3309] [3310] [3311] [3312] [3313]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13672--13672
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3314]
Underfull \hbox (badness 10000) in paragraph at lines 13699--13702
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3315]
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[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13742--13749
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13799--13799
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3316]
Underfull \hbox (badness 10000) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13806--13809
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13834--13837
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13834--13837
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3317]
Underfull \hbox (badness 10000) in paragraph at lines 13914--13917
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3318]
Underfull \hbox (badness 1472) in paragraph at lines 13939--13946
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3319]
Underfull \hbox (badness 10000) in paragraph at lines 14008--14010
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3320] [3321] [3322] [3323]
Underfull \hbox (badness 1215) in paragraph at lines 14288--14290
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3324] [3325] [3326] [3327]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14532--14532
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3328] [3329] [3330] [3331] [3332] [3333] [3334] [3335] [3336]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15185 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15185 ...Extract Random Effects}{random.effects}
                                                   [3337] [3338] [3339]
[3340] [3341] [3342] [3343] [3344] [3345] [3346]
Underfull \hbox (badness 2126) in paragraph at lines 15825--15829
[]\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199
7). Phar-ma-coki-net-
[3347]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15833--15833
 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15852--15852
 []    \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718
4, tol = 1.5e-5),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15853--15853
 []              \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),              
   tol = 7e-7)[] 
[3348]
Underfull \hbox (badness 1009) in paragraph at lines 15883--15892
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3349] [3350]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16030--16030
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3351] [3352] [3353] [3354] [3355]
Underfull \hbox (badness 10000) in paragraph at lines 16365--16371
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3356]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16396--16396
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3357] [3358] [3359] [3360] [3361] [3362] [3363]
Underfull \hbox (badness 1728) in paragraph at lines 16885--16888
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3364] [3365] [3366] [3367] [3368]
Underfull \hbox (badness 1867) in paragraph at lines 17220--17229
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" 
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener
al
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\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3369]
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[]\T1/pcr/m/n/10 "Constant plus power of variance
Underfull \hbox (badness 10000) in paragraph at lines 17292--17293
[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3370] [3371] [3372] [3373]
Underfull \hbox (badness 10000) in paragraph at lines 17542--17550
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstProp[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varFixed[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]\T1/ptm/m/n/10 ,
[3374] [3375] [3376] [3377]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17814--17814
 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17816--17816
 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[] 
[3378] [3379] [3380] [3381] [3382] [3383]
Underfull \hbox (badness 10000) in paragraph at lines 18252--18262
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18252--18262
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3384]
Underfull \hbox (badness 3579) in paragraph at lines 18290--18295
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3385]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3386]
Underfull \hbox (badness 3579) in paragraph at lines 18417--18422
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3387]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3388]
Underfull \hbox (badness 3579) in paragraph at lines 18543--18548
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18576--18585
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18576--18585
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3389]
Underfull \hbox (badness 3579) in paragraph at lines 18615--18620
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3390] [3391]
Underfull \hbox (badness 1009) in paragraph at lines 18761--18770
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3392] [3393]
Underfull \hbox (badness 1009) in paragraph at lines 18893--18902
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3394] [3395] [3396] [3397] [3398] [3399] [3400] [3401] [3402]) (./nnet-pkg.tex
Chapter 26.
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<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
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                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3403]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3404] [3405] [3406]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3407]
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 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 
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 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3408] [3409]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3410]) (./rpart-pkg.tex
Chapter 27.
[3411] [3412] [3413] [3414]
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 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3415] [3416] [3417] [3418]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3419] [3420]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3421] [3422]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3423]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3424] [3425] [3426]
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 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 
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 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3427]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3428]
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 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 
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 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3429] [3430] [3431] [3432] [3433] [3434]
Underfull \hbox (badness 1565) in paragraph at lines 1745--1748
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3435] [3436]
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 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3437] [3438] [3439]) (./spatial-pkg.tex [3440]
Chapter 28.
[3441] [3442] [3443] [3444] [3445] [3446]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3447] [3448] [3449] [3450] [3451] [3452] [3453] [3454] [3455] [3456] [3457]
[3458] [3459]) (./survival-pkg.tex [3460]
Chapter 29.
[3461] [3462]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
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 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
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 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3463] [3464]
Underfull \hbox (badness 6412) in paragraph at lines 282--284
[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as 
long as
[3465] [3466]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.382 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.382 ... Myelogenous Leukemia survival data}{aml}
                                                   [3467]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 485--485
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3468]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3469] [3470]
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[3471] [3472]
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 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 792--792
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3473] [3474]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 935--935
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3475] [3476] [3477]
Underfull \hbox (badness 1097) in paragraph at lines 1106--1108
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3478] [3479]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3480]
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 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter, 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1308 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3481]
Underfull \hbox (badness 10000) in paragraph at lines 1356--1360
[]\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea
led by
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 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1408--1408
 []  \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[] 
[3482] [3483] [3484]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1575--1575
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1622--1622
 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE) 
[3485] [3486] [3487] [3488] [3489]
Underfull \hbox (badness 10000) in paragraph at lines 1938--1953
[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
Underfull \hbox (badness 7486) in paragraph at lines 1938--1953
\T1/ptm/m/n/10 some cod-ing guides and prepend \T1/pcr/m/n/10 survival:: \T1/pt
m/m/n/10 onto ev-er-thing, in-clud-ing the spe-
Underfull \hbox (badness 10000) in paragraph at lines 1938--1953
\T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t
ime,status) ~ age +
[3490]
Underfull \hbox (badness 1337) in paragraph at lines 2022--2026
[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3491]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2649--2649
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
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 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3500] [3501] [3502]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2908--2908
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3503] [3504] [3505]
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[3506] [3507]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3249--3249
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3508]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3284--3284
 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 
Underfull \hbox (badness 1389) in paragraph at lines 3298--3300
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
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 []        \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[] 
[3509] [3510]
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 []                 \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3511] [3512]
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 [] [] 
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[3514]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3706--3706
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3515] [3516] [3517] [3518] [3519] [3520] [3521]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4095--4095
 []                    \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3522] [3523]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4241--4241
 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[] 
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 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4250--4250
 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1])  # differences: yhat[2:
4] - yhat[1][] 
[3524]
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[3526] [3527] [3528] [3529] [3530]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4667--4667
 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3531] [3532] [3533]
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 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3534]
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 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3535]
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 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3536]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3537]
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 []  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[] 
[3538]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3539] [3540]
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 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1
=FALSE, ...) 
[3541] [3542]
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 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
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 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3543] [3544]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3545]
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3546]
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 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
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 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3547] [3548] [3549] [3550] [3551] [3552]
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 []       \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[] 
[3553] [3554] [3555]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
Underfull \hbox (badness 1043) in paragraph at lines 6491--6494
\T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3556] [3557] [3558] [3559] [3560]
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 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6800--6800
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[] 
[3561] [3562]
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 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE) 
[3563]
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 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)]  # rem
ove duplicates[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7008 ...ata from a soldering experiment}{solder}
                                                   [3564] [3565]
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 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3566] [3567] [3568] [3569] [3570]
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 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
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 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3571] [3572] [3573] [3574]
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 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3575] [3576] [3577] [3578]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3579] [3580]
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 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)", 
[3581]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3582] [3583]
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 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3584]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3585]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3586] [3587] [3588] [3589]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
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 []        \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
 ctype,[] 
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
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 []        \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[] 
[3593]
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[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
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\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
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\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
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[3595]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3596] [3597] [3598] [3599] [3600]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3601]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # 
use concordance 
[3602] [3603] [3604]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3605]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3606] [3607] [3608]
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 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3609]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
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 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3610] [3611] [3612] [3613] [3614]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3615] [3616] [3617] [3618] [3619] [3620] [3621]
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 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3622] [3623] [3624]) (./fullrefman.ind [3625] [3626] [3627] [3628] [3629]
[3630] [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640]
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[3649]
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3650] [3651] [3652] [3653] [3654] [3655]
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3656]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3657] [3658] [3659] [3660] [3661] [3662] [3663] [3664] [3665]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
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[3666]
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[3667]
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[]\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method 
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method 
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method 
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[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method 
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[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 
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[]\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method 
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[]\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method 
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[]\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method 
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[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method 
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[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method 
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[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method 
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method 
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method 
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[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method 
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[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method 
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[]\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method 
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[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method 
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[]\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method 
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[]\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method 
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[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method 
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method 
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[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method 
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[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings 
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[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method 
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}] (./fullrefman.toc (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
[18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32]
[33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
[48] [49]) [50] [1] [2] (./base-pkg.tex
Chapter 1.
[3] [4]
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10
 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-
wise, it is \T1/pcr/m/n/10 (double.base ^
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It
Underfull \hbox (badness 1028) in paragraph at lines 143--151
\T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt
m/m/n/10 if \T1/pcr/m/n/10 double.base
Underfull \hbox (badness 2980) in paragraph at lines 143--151
\T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/pcr/m/n/10 (double.base
Underfull \hbox (badness 1394) in paragraph at lines 143--151
\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As
Underfull \hbox (badness 1668) in paragraph at lines 154--161
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5]
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[]\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]("long.double") \T1/
ptm/m/n/10 is true, there are 10 such
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\T1/pcr/m/n/10 *.exponent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 *.min.exp\T1/ptm/m/n/1
0 , and \T1/pcr/m/n/10 *.max.exp\T1/ptm/m/n/10 , com-puted en-tirely anal-o-gou
sly to their
[6] [7]
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[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8] [9] [10]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11]
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 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v
alue = TRUE)[] 
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 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i
gnore.case = TRUE)[] 
[12] [13] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14]
[15] [16]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 922--922
 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 
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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[17] [18] [19] [20] [21] [22] [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [24] [25]
Underfull \hbox (badness 10000) in paragraph at lines 1567--1573
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[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[26] [27]
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 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[28]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
 than 256 (or
[29] [30]
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[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh
ich can be co-erced by
[31] [32]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
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[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[33] [34] [35] [36]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[37]
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 []  \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo
ne1970.tab"),[] 
[38]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by
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[][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via
[39]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[40] [41] [42]
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 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE), 
[43] [44] [45] [46] [47] [48] [49] [50] [51]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3399--3399
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 
[52]
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 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 
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 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
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 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3439--3439
 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3442--3442
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[53] [54] [55] [56] [57] [58]
Underfull \hbox (badness 10000) in paragraph at lines 3888--3890
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[59] [60] [61] [62] [63] [64] [65]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject
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\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[66] [67]
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 []             \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[] 
[68]
Underfull \hbox (badness 4595) in paragraph at lines 4542--4545
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[69] [70]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4704--4704
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
Underfull \hbox (badness 1199) in paragraph at lines 4735--4741
[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
[71]
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[72] [73]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[74] [75] [76] [77]
Underfull \hbox (badness 2521) in paragraph at lines 5178--5180
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[78] [79] [80] [81] [82] [83]
Underfull \hbox (badness 10000) in paragraph at lines 5600--5608
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[84] [85] [86] [87] [88] [89] [90] [91] [92]
Underfull \hbox (badness 1796) in paragraph at lines 6171--6179
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
[93] [94] [95]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
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 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows  \TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] 
[96] [97]
Underfull \hbox (badness 1635) in paragraph at lines 6573--6576
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing
[98]
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[99] [100]
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 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[101]
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[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
[102] [103]
Underfull \hbox (badness 1997) in paragraph at lines 6972--6977
[]\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1
0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x
zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC
onnection\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[104] [105] [106]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move
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\T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and 
web-pages gen-er-ated by
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\T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re
c-om-mended) when writ-ing
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\T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write
Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 7212--7214
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/pcr/m/n/10 descriptio
n = "clipboard" \T1/ptm/m/n/10 in mode \T1/pcr/m/n/10 "r" \T1/ptm/m/n/10 only. 
This
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\T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http
s : / / specifications . freedesktop .
Underfull \hbox (badness 1735) in paragraph at lines 7254--7261
\T1/pcr/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as \
T1/pcr/m/n/10 "X11_secondary"\T1/ptm/m/n/10 . On most sys-
[107] [108]
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Underfull \vbox (badness 10000) has occurred while \output is active [110]
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 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[111]
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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[112] [113] [114]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[115] [116] [117]
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 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[118] [119] [120] [121]
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 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[122]
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[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8306--8316
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be
[123]
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[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[124] [125]
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 []                 \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[] 
[126] [127] [128] [129]
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[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times
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\T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10
 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz =
[130] [131] [132] [133] [134] [135]
Underfull \hbox (badness 10000) in paragraph at lines 9278--9282
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[136] [137]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
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 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
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 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
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 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[138] [139]
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[]\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact
er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by
Underfull \hbox (badness 6063) in paragraph at lines 9554--9556
[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n
/10 formula[][][]\T1/ptm/m/n/10 s, with
[140] [141] [142]
Underfull \hbox (badness 1603) in paragraph at lines 9779--9782
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[143] [144] [145] [146] [147] [148] [149] [150] [151]
Underfull \hbox (badness 1917) in paragraph at lines 10394--10399
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
[152]
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 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10450--10450
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[153] [154]
Underfull \hbox (badness 1168) in paragraph at lines 10552--10557
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
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[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as
[155] [156]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
[157]
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 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[158]
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 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] 
[159] [160]
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 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[161] [162] [163]
Underfull \hbox (badness 6396) in paragraph at lines 11218--11226
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[164] [165] [166]
Underfull \hbox (badness 10000) in paragraph at lines 11444--11447
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[167] [168] [169] [170] [171] [172] [173]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11899--11899
 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[] 
[174] [175] [176]
Underfull \hbox (badness 5288) in paragraph at lines 12150--12152
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
[177]
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[178] [179]
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment
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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[180] [181]
Underfull \hbox (badness 10000) in paragraph at lines 12482--12484
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13328--13328
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 2221) in paragraph at lines 13791--13800
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
Underfull \hbox (badness 1635) in paragraph at lines 13791--13800
\T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l
ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all
[200] [201] [202]
Underfull \hbox (badness 2253) in paragraph at lines 14052--14054
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[203] [204]
Underfull \hbox (badness 2573) in paragraph at lines 14172--14174
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr
/m/n/10 fsep =
[205] [206]
Underfull \hbox (badness 10000) in paragraph at lines 14331--14333
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[207] [208]
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[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14459--14462
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[209]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[210]
Underfull \hbox (badness 10000) in paragraph at lines 14599--14602
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 14609--14609
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[211]
Underfull \hbox (badness 10000) in paragraph at lines 14675--14678
[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class
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 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[212]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
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[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 , where
Underfull \hbox (badness 7273) in paragraph at lines 14745--14752
\T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi
v-a-lent to \T1/pcr/m/n/10 apply(
Underfull \hbox (badness 3965) in paragraph at lines 14753--14757
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[213] [214] [215]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14918--14918
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[216] [217] [218]
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 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 
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 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[219]
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[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[220]
Underfull \hbox (badness 6944) in paragraph at lines 15337--15340
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,
[221]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[222] [223]
Underfull \hbox (badness 10000) in paragraph at lines 15500--15502
[]\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos
-si-bly for-mat-ted) num-bers, also in
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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[224]
Underfull \hbox (badness 2790) in paragraph at lines 15533--15536
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
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[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[225]
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[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls
Underfull \hbox (badness 4954) in paragraph at lines 15639--15641
\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this
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[]\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1
23.45,mode =
[226]
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[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
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\T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15786--15786
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
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 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you 
want see the effect[] 
[229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240]
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 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[241]
Underfull \hbox (badness 2418) in paragraph at lines 16751--16755
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
Underfull \hbox (badness 6510) in paragraph at lines 16758--16761
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle
[242]
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[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[243] [244] [245]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
[246]
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[247] [248] [249] [250]
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 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 17408--17408
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
[252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17464--17464
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[253] [254] [255] [256]
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 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9))) 
[257]
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 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[] 
[258] [259] [260]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18092--18092
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[261] [262] [263] [264]
Underfull \hbox (badness 2285) in paragraph at lines 18426--18428
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
[265]
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 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[266] [267]
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 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
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 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
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 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 
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 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
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 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
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 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] 
[270] [271] [272]
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[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[273] [274] [275] [276] [277]
Underfull \hbox (badness 10000) in paragraph at lines 19290--19296
Underfull \hbox (badness 10000) in paragraph at lines 19303--19305
[]\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac
le . com / cd / E19957-[]01 / 806-[]3568 / ncg _
[278] [279] [280]
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[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[281] [282]
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 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[286]
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 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19848--19848
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
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[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[295] [296] [297] [298] [299] [300] [301]
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[]\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/
n/10 and
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[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
[302]
Underfull \hbox (badness 10000) in paragraph at lines 20951--20955
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-
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\T1/ptm/m/n/10 tory `\T1/pcr/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/pcr
/m/n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (o
r
[303] [304]
Underfull \hbox (badness 10000) in paragraph at lines 21100--21104
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-
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[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21357--21361
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[309]
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[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the
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\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of
Underfull \hbox (badness 5133) in paragraph at lines 21427--21432
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 21427--21432
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[310] [311]
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[312]
Underfull \hbox (badness 3343) in paragraph at lines 21659--21663
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[313] [314]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21800--21800
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
[315]
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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 prob = 0.2))),[] 
[316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21922--21922
 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
 same names ![] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 21925--21925
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
[317]
Underfull \hbox (badness 6380) in paragraph at lines 21970--21975
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[318]
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[319]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 22098--22098
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[320] [321]
Underfull \hbox (badness 1400) in paragraph at lines 22266--22270
[][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][]
 \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do
uble[][][] \T1/ptm/m/n/10 (class
[322] [323]
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[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. In nu-meric and
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\T1/ptm/m/n/10 com-plex vec-tors, ze-ros are \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/1
0 and non-zero val-ues are \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 . For [][]\T1/pcr/
m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 10000) in paragraph at lines 22436--22444
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing
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\T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t
rue") \T1/ptm/m/n/10 are re-garded as true,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 23093--23093
 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary =  r ), complex(real =  
r , imaginary = NA ),[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 23094--23094
 []        \T1/pcr/m/n/9 complex(real =  r , imaginary = NaN), complex(real = N
aN, imaginary =  r ))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 23097--23097
 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] 
[334] [335]
Underfull \hbox (badness 1655) in paragraph at lines 23221--23225
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[336] [337] [338] [339]
Underfull \hbox (badness 2277) in paragraph at lines 23470--23473
[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][]
\T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod()
 \T1/ptm/m/n/10 are typ-i-cally prefer-able.
[340] [341]
Underfull \hbox (badness 10000) in paragraph at lines 23601--23604
[]\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc
r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.
0,
[342] [343] [344] [345] [346] [347] [348]
Underfull \hbox (badness 1484) in paragraph at lines 24057--24065
[]\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less 
the OS's de-fault has been
Underfull \hbox (badness 1152) in paragraph at lines 24057--24065
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / docs . microsoft . com / en-[]gb /
[349]
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 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[350] [351] [352] [353] [354] [355] [356]
Underfull \hbox (badness 1448) in paragraph at lines 24648--24656
\T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T
1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive =
[357] [358]
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[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[359]
Underfull \hbox (badness 7308) in paragraph at lines 24840--24846
[]\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing
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\T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) 
\T1/ptm/m/n/10 which are also given by
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[][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 
. If the en-vi-ron-ment is used as a hash
Underfull \hbox (badness 10000) in paragraph at lines 24850--24853
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:
Underfull \hbox (badness 10000) in paragraph at lines 24850--24853
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as \T1/pcr/m/n/10 z
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[362] [363] [364]
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[]\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by
[365] [366] [367]
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\T1/ptm/m/n/10 tion \T1/pcr/m/n/10 GetFinalPathNameByHandle \T1/ptm/m/n/10 and 
in case of an er-ror (such as in-suf-fi-cient per-
[368] [369] [370] [371] [372]
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
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[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-
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\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
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 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 
[373]
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 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[374]
Underfull \hbox (badness 10000) in paragraph at lines 25832--25838
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.
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\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in%
[375]
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 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] 
[376] [377]
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[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][]
[378] [379] [380]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[381] [382] [383] [384]
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[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[385] [386]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 26706--26714
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[387] [388]
Underfull \hbox (badness 3271) in paragraph at lines 26925--26928
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[389] [390] [391]
Underfull \hbox (badness 3138) in paragraph at lines 27231--27237
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by
[392]
Underfull \hbox (badness 1194) in paragraph at lines 27244--27247
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and
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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
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[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[393]
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS
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\T1/ptm/m/n/10 build), \T1/pcr/m/n/10 "mac.binary" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS
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\T1/ptm/m/n/10 builds). (\T1/pcr/m/n/10 "mac.binary.el-capitan"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 5091) in paragraph at lines 27347--27353
\T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina
ry.universal" \T1/ptm/m/n/10 are no longer
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[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to
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\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a CRAN
Underfull \hbox (badness 2837) in paragraph at lines 27362--27369
\T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li
ke \T1/pcr/m/n/10 local({r
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\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[394] [395] [396] [397]
Underfull \vbox (badness 10000) has occurred while \output is active [398]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27710--27710
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 
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[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion
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\T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A
[c(arrayindex.x,arrayindex.y)] =
[399] [400]
Underfull \hbox (badness 10000) in paragraph at lines 27870--27873
[]\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
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\T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for
e be re-garded as trans-form-ing
[401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 28152--28158
[][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/
n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Underfull \hbox (badness 2495) in paragraph at lines 28152--28158
[][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][]
 \T1/ptm/m/n/10 which con-cate-nates and
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 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 
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 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
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 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
 ' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling :
[] 
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 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[] 
[405] [406] [407]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28377--28377
 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow()  # same as nrow(subset(mt
cars, cyl == 4))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28386--28386
 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so 
is not evaluated[] 
[408]
Underfull \hbox (badness 1360) in paragraph at lines 28441--28445
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type =
[409] [410] [411] [412] [413] [414]
Underfull \hbox (badness 2005) in paragraph at lines 28836--28840
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/cmtt/m/n/10 `\T1/pc
r/m/n/10 name\TS1/cmtt/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr
/m/n/10 get[][][](name,envir =
[415]
Underfull \hbox (badness 1796) in paragraph at lines 28904--28907
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[416] [417] [418] [419]
Underfull \hbox (badness 10000) in paragraph at lines 29108--29111
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 29803--29803
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[430] [431] [432] [433]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30094--30094
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 
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 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 
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 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
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 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
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 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [434]
[435]
Underfull \hbox (badness 7415) in paragraph at lines 30200--30204
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[436]
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 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[437]
Underfull \hbox (badness 3713) in paragraph at lines 30390--30401
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[438] [439]
Underfull \hbox (badness 1248) in paragraph at lines 30534--30541
\T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM
 Trans-ac-tions on Mod-el-ing and Com-puter
Underfull \hbox (badness 10000) in paragraph at lines 30534--30541
\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh
ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
[440] [441]
Underfull \hbox (badness 1533) in paragraph at lines 30652--30655
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[442] [443]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 30797--30797
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 30815--30826
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[444] [445]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30959--30959
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 
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 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 
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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30963--30963
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30964--30964
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 
[446]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30971--30971
 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[447] [448] [449] [450]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 31279--31279
 []\T1/pcr/m/n/9 ## Bit representation  [ sign | exponent | mantissa ] of doubl
e prec numbers :[] 
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 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
 # split one double[] 
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 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 31292--31292
 []\T1/pcr/m/n/9 d2b  <- function(x) vapply(as.double(x), function(x)          
 numToBits(x) , raw(64L))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [451]
[452]
Underfull \hbox (badness 4048) in paragraph at lines 31387--31392
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:
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\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2080) in paragraph at lines 31924--31934
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 infoRDS\T1/ptm/m/n/10 , an \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 list with el-e-ments \T1/pcr/m/n/10 version \T1/ptm/m/n/10 (ver
-sion num-ber, cur-rently 2 or 3),
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 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 7558) in paragraph at lines 32477--32481
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 32487--32489
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
Underfull \hbox (badness 10000) in paragraph at lines 32498--32500
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / 
pubs . opengroup . org / onlinepubs /
[468]
Underfull \hbox (badness 1975) in paragraph at lines 32501--32505
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 pcre2pattern \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 pcrepattern man \T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m/n/10 ht
tps : / / www .
[469] [470] [471] [472] [473]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32872--32872
 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3)         # length 24, 3 complete 
replications[] 
[474]
Underfull \hbox (badness 10000) in paragraph at lines 32943--32947
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[475] [476] [477]
Underfull \hbox (badness 2302) in paragraph at lines 33169--33174
[]\T1/pcr/m/n/10 signif \T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-me
nt to the spec-i-fied num-ber of sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for \T1/pcr/m/n/10 numeric x\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 signif(x,dig) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 round(x,
dig
[478] [479]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33302--33302
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 33305--33305
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[480] [481] [482] [483] [484] [485] [486]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 33746--33746
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[487] [488] [489] [490] [491] [492]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 34183--34183
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[493] [494]
Underfull \hbox (badness 1158) in paragraph at lines 34287--34292
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions
[495] [496]
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 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[497] [498] [499]
Underfull \hbox (badness 8151) in paragraph at lines 34732--34735
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 .
[500] [501] [502] [503]
Underfull \hbox (badness 10000) in paragraph at lines 34947--34952
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10
 gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by =
[504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515]
[516] [517] [518]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 35936--35936
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[519] [520] [521]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36188--36188
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 36190--36190
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[522]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/
m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/
10 , see also
Underfull \hbox (badness 5050) in paragraph at lines 36233--36239
[][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p
tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[523] [524]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 36344--36344
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[525] [526] [527] [528] [529]
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 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36700--36700
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[530] [531] [532]
Underfull \hbox (badness 10000) in paragraph at lines 36925--36927
[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
[533] [534] [535]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 37152--37152
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 37153--37153
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[536] [537] [538] [539]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 37420--37420
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[540]
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[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
 saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert 
a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 37511--37521
\T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o
n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 37511--37521
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an 
en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-
ing
[541]
Underfull \hbox (badness 10000) in paragraph at lines 37557--37563
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 37557--37563
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 37557--37563
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
Underfull \hbox (badness 1460) in paragraph at lines 37572--37579
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 37572--37579
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 37572--37579
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[542] [543] [544]
Underfull \hbox (badness 1484) in paragraph at lines 37804--37808
[]\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/
m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[545]
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 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[546] [547] [548] [549] [550] [551] [552] [553] [554]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 38446--38446
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[555] [556] [557]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 38696--38696
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[558]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38740--38740
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[559] [560] [561] [562] [563] [564]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 39174--39174
 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 39177--39177
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[565]
Underfull \hbox (badness 10000) in paragraph at lines 39228--39235
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
Underfull \hbox (badness 10000) in paragraph at lines 39228--39235
\T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][]
[]() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ).
[566]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39281--39281
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[567] [568] [569] [570] [571]
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 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[572] [573]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39757--39757
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[574]
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 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
Underfull \hbox (badness 2293) in paragraph at lines 39825--39831
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 39825--39831
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the \T1/pcr/m/n/10 glob \T1/ptm/m/n/10 sys-tem call.
Underfull \hbox (badness 4792) in paragraph at lines 39844--39849
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 39844--39849
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[575] [576] [577] [578]
Underfull \hbox (badness 10000) in paragraph at lines 40132--40136
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and
[579]
Underfull \hbox (badness 1584) in paragraph at lines 40147--40150
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[580] [581]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 40285--40285
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[582]
Overfull \hbox (19.22812pt too wide) in paragraph at lines 40362--40362
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[583] [584]
Underfull \hbox (badness 1082) in paragraph at lines 40506--40509
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[585] [586] [587]
Underfull \hbox (badness 1038) in paragraph at lines 40697--40700
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[588] [589] [590] [591] [592]
Underfull \hbox (badness 1442) in paragraph at lines 41061--41065
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout =
 TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout =
[593] [594] [595] [596]
Underfull \hbox (badness 4096) in paragraph at lines 41311--41314
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[597]
Underfull \hbox (badness 7888) in paragraph at lines 41425--41429
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10
 length(bin) >
[598] [599] [600]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 41579--41579
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (35.4281pt too wide) in paragraph at lines 41581--41581
 []            \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[
] 
Overfull \hbox (55.67578pt too wide) in paragraph at lines 41583--41583
 []                 \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = 
NULL), dim=4, dimnames=list(as.character(2:5)))))[] 
Underfull \hbox (badness 10000) in paragraph at lines 41596--41598
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[601]
Underfull \hbox (badness 10000) in paragraph at lines 41676--41679
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[602] [603]
Underfull \hbox (badness 3872) in paragraph at lines 41794--41797
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[604]
Underfull \hbox (badness 5475) in paragraph at lines 41860--41864
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
[605] [606] [607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 42283--42290
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 42339--42348
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 42339--42348
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
[611]
Underfull \hbox (badness 1082) in paragraph at lines 42349--42361
\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 
' in that di-rec-tory states the ver-sion. That op-tion is
Underfull \hbox (badness 1337) in paragraph at lines 42422--42430
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
[612]
Underfull \hbox (badness 10000) in paragraph at lines 42431--42434
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
Underfull \hbox (badness 3460) in paragraph at lines 42485--42488
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 42489--42491
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 42498--42498
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[613] [614] [615]
Underfull \hbox (badness 10000) in paragraph at lines 42719--42721
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[616] [617]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42841--42841
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42843--42843
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
[618] [619]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 42944--42944
 []                                           \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 42946--42946
 []                                           \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[] 
[620] [621] [622]
Underfull \hbox (badness 6542) in paragraph at lines 43220--43222
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[623] [624]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 43339--43339
 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[625]
Underfull \hbox (badness 1708) in paragraph at lines 43407--43415
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 43407--43415
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
[626]
Underfull \hbox (badness 4859) in paragraph at lines 43437--43442
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[627]
Underfull \hbox (badness 3895) in paragraph at lines 43499--43511
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 43499--43511
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[628] [629] [630] [631] [632]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 43821--43821
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[633] [634] [635] [636] [637] [638]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44290--44290
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[639]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 44299--44299
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[] 
Underfull \hbox (badness 2057) in paragraph at lines 44365--44371
[][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.append[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 file.copy[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.create[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.exists[][][]\T1/ptm/m/n/10 ,
[640]
Underfull \hbox (badness 3861) in paragraph at lines 44374--44379
[][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 normalizePath[][][]\T1/ptm/m/n/10
 , [][]\T1/pcr/m/n/10 path.expand[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pipe
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Sys.glob[][][]\T1/ptm/m/n/10 ,
[641]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 44467--44467
 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] 
[642]
Underfull \hbox (badness 1803) in paragraph at lines 44520--44523
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 3471) in paragraph at lines 44524--44531
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and
[643] [644] [645]
Underfull \hbox (badness 3668) in paragraph at lines 44739--44741
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[646]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 44845--44845
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[647]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 44920--44920
 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] 
[648]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 44928--44928
 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
 There were 105 warnings ...[] 
[649]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 45022--45022
 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 45026--45026
 []\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings
AsFactors = FALSE) {[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 45027--45027
 []    \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa
ctors=stringsAsFactors)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45034--45034
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler:  Date -> Matrix
 - dropping time info {sec,min,hour, isdst}[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 45037--45037
 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] 
[650]
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[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,
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\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
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\T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m
a-trix whose rows each
[651]
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[]\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor 
\T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/
ptm/m/n/10 and
[652]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[653] [654] [655] [656] [657] [658] [659]
Underfull \hbox (badness 2846) in paragraph at lines 45686--45690
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
[660]
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[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[661]) (./compiler-pkg.tex [662]
Chapter 2.
[663]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us
ed to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt
m/m/n/10 , and
[664] [665] [666]) (./datasets-pkg.tex
Chapter 3.
[667] [668] [669] [670] [671]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[672]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
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[674] [675] [676]
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 []           \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[] 
[677]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[678] [679]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 837--840
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[680] [681] [682]
Underfull \hbox (badness 1097) in paragraph at lines 1037--1041
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[683]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[684] [685] [686] [687] [688]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[689] [690]
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[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[691] [692] [693]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[694]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 
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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[695] [696]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 
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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[697] [698] [699] [700]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[701] [702] [703]
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[704] [705] [706] [707] [708]
Overfull \hbox (48.81013pt too wide) in paragraph at lines 2725--2728
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[709]
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[710]
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[712] [713] [714] [715]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[716] [717] [718] [719] [720] [721] [722] [723]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[724] [725]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[726]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[727]
Overfull \vbox (15.49593pt too high) has occurred while \output is active
[728]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740]
[741] [742]) (./grDevices-pkg.tex
Chapter 4.
[743] [744] [745] [746]
Underfull \hbox (badness 1365) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to
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[]\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in
[747] [748]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to
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\T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea
s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1
[749] [750]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[751] [752] [753] [754] [755] [756] [757] [758] [759] [760]
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[761] [762] [763]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
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[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[764] [765] [766] [767] [768] [769] [770] [771]
Underfull \hbox (badness 1565) in paragraph at lines 1893--1898
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not
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\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[772]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-
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\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[773] [774]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[775] [776]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[777] [778]
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\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[779] [780]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
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 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE) 
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 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[] 
[782] [783] [784] [785] [786]
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[788] [789] [790] [791]
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 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[792]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 
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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[793] [794]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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\T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le
ss that's zero where it uses in-creas-ingly more ex-treme sym-
[795] [796]
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 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE)[] 
[797]
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 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[] 
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 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[] 
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 []    \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab =
 "", main=main)[] 
[798]
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 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 
[799]
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[]\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 ,
[800]
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[]\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we
ll for shad-ing points or lines in up to five groups,
Underfull \hbox (badness 10000) in paragraph at lines 3862--3866
\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space 
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[801]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[803] [804] [805] [806] [807]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[808] [809] [810] [811] [812] [813]
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[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /
[814] [815]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[816] [817]
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[818]
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as
[819]
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), \T1/pcr/m/n/10 "CP1251.enc"
[820]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[821] [822] [823]
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[824] [825]
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\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
Underfull \hbox (badness 2221) in paragraph at lines 5620--5622
[]\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for
[826]
Underfull \hbox (badness 5388) in paragraph at lines 5678--5680
[]\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr
/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[827] [828]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5779--5779
 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[829]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[830] [831]
Underfull \hbox (badness 10000) in paragraph at lines 5977--5979
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[832] [833] [834] [835] [836]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6344--6344
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 
Underfull \hbox (badness 10000) in paragraph at lines 6358--6361
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[837] [838] [839] [840] [841] [842]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6693--6693
 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6700--6700
 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[843] [844] [845] [846]
Underfull \hbox (badness 10000) in paragraph at lines 6963--6968
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1803) in paragraph at lines 6963--6968
\T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y
pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2941) in paragraph at lines 6963--6968
\T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/
ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T
1/ptm/m/n/10 and
[847]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7069--7069
 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[848]
Underfull \hbox (badness 3590) in paragraph at lines 7108--7111
[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 2393) in paragraph at lines 7108--7111
\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one 
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7119--7119
 []    \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[] 
[849]
Underfull \hbox (badness 1189) in paragraph at lines 7184--7186
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[850]
Underfull \hbox (badness 10000) in paragraph at lines 7289--7291
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[851]
Underfull \hbox (badness 10000) in paragraph at lines 7335--7342
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and
Underfull \hbox (badness 2469) in paragraph at lines 7335--7342
\T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy
s-tems which have the Wine
[852]
Underfull \hbox (badness 5607) in paragraph at lines 7419--7423
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[853]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7471--7471
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[854] [855]
Underfull \hbox (badness 5637) in paragraph at lines 7603--7609
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1721) in paragraph at lines 7636--7639
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[856] [857] [858]
Underfull \hbox (badness 1231) in paragraph at lines 7805--7807
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[859] [860]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 4647) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use \T1/pcr/m/n/10 library(help =
[861] [862] [863]
Underfull \hbox (badness 3792) in paragraph at lines 177--180
[]\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b
e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point
[864] [865] [866] [867]
Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450
 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 
Underfull \hbox (badness 4048) in paragraph at lines 482--488
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[868] [869]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580
 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[870]
Underfull \hbox (badness 10000) in paragraph at lines 694--698
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 694--698
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if
[871] [872]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818
 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[873] [874] [875]
Underfull \hbox (badness 10000) in paragraph at lines 964--968
[][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10
 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able.
Overfull \hbox (133.98029pt too wide) in paragraph at lines 981--981
 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 983--983
 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 985--985
 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[876] [877] [878] [879]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269
 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. 
outside hinges"):[] 
[880] [881] [882]
Underfull \hbox (badness 1024) in paragraph at lines 1431--1439
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
Underfull \hbox (badness 3375) in paragraph at lines 1465--1467
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[883] [884]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1536--1536
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1543--1543
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[885] [886] [887] [888] [889]
Underfull \hbox (badness 10000) in paragraph at lines 1846--1852
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1866--1866
 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1878--1878
 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1894--1894
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1903--1903
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[890] [891]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1988--1988
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[892] [893]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2117--2117
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2122--2122
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[894] [895]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296
 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8, 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 2297--2297
 []         \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[] 
[896]
Underfull \hbox (badness 1430) in paragraph at lines 2328--2330
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/pcr/m/n/10 "n
" \T1/ptm/m/n/10 to sup-press and see also
[897]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2409--2409
 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 
Underfull \hbox (badness 1009) in paragraph at lines 2421--2428
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[898]
Underfull \hbox (badness 7273) in paragraph at lines 2503--2507
[][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T
1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and
[899] [900] [901] [902]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2751--2751
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[903]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2788--2788
 []     \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = 
NULL,[] 
[904] [905]
Underfull \hbox (badness 1226) in paragraph at lines 2913--2917
\T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr
/m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2966--2966
 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] 
[906]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2970--2970
 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
Underfull \hbox (badness 10000) in paragraph at lines 3022--3025
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[907] [908] [909]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3227--3227
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3232--3232
 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[910] [911]
Underfull \hbox (badness 10000) in paragraph at lines 3374--3379
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3374--3379
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3374--3379
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[912] [913] [914]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3560--3560
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3579--3579
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[915]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3583--3583
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[916] [917]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3760--3760
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3761--3761
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[918]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3800--3800
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
Underfull \vbox (badness 10000) has occurred while \output is active [919]
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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3860--3860
 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3862--3862
 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3870--3870
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[920]
Underfull \hbox (badness 10000) in paragraph at lines 3933--3937
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m
/n/10 type %in%
[921] [922]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4045--4045
 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[923] [924]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4199--4199
 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[] 
[925]
Underfull \hbox (badness 3930) in paragraph at lines 4278--4280
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[926] [927] [928] [929] [930]
Underfull \hbox (badness 1286) in paragraph at lines 4589--4592
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[931] [932]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 
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 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[933]
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\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[934] [935]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[936] [937]
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[938 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//mai.pdf>]
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[939 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//oma.pdf>]
[940]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[941]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 
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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
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[943] [944] [945] [946] [947]
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 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
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 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 
[948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5891 \aliasA{plot}{plot.default}{plot}
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 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[954] [955] [956] [957] [958] [959]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[960] [961]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][] 
[962 </builddir/build/BUILD/R-4.1.0/library/graphics/help/figures//pch.pdf>]
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[963]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[965]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 
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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[966]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[967] [968] [969] [970]
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[971] [972] [973] [974] [975] [976]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 
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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[977]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[978] [979] [980] [981] [982]
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us  =  FALSE,[] 
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 
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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[983] [984] [985]
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 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 
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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[986] [987]
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 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 
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[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[988]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[989]
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[990] [991]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[992] [993]
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 []     \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est fa�ile: 
R�gles, Libert�, Egalit�, Fraternit�...")[] 
[994]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color
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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[997] [998]
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 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[999]) (./grid-pkg.tex [1000]
Chapter 6.
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,
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\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[1009]
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
 to the
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it(1, "inches")))[] 
[1016] [1017] [1018]
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, height=0.5,[] 
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), name="B"),[] 
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, height=0.5,[] 
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), name="C"),[] 
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, height=0.5,[] 
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), name="D")),[] 
[1019]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1020] [1021] [1022]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[1023] [1024] [1025] [1026] [1027] [1028] [1029]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1030] [1031] [1032]
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ck"), name="r1")[] 
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), name="r2")[] 
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te"), name="r3")[] 
[1033]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[1034]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
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[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[1035] [1036] [1037]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[1038] [1039] [1040]
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1041]
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[1042] [1043]
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="vp1::vp2")),[] 
[1044]
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[1045] [1046] [1047]
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, "inches"),[] 
[1048] [1049] [1050] [1051] [1052]
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1053] [1054]
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c("left", "bottom")))[] 
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[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[1055] [1056]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1057] [1058] [1059]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 
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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
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 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
[1072]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1073]
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[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[1074] [1075] [1076]
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it(1, "inches")))[] 
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097]
[1098]
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[]\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo
r unit ob-jects. In par-
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\T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects (
e.g., \T1/pcr/m/n/10 unit(1,"npc")
[1099] [1100] [1101] [1102] [1103]
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 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[] 
[1104]
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[1105]
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[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[1106] [1107]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/pcr/m/n/10 depth
[1108]
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[1110] [1111]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1112]) (./methods-pkg.tex
Chapter 7.
[1113] [1114]
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\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c
o-erce meth-ods work. Use
[1115] [1116] [1117]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1118] [1119]
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 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 
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 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1120]
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 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 
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 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 
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 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 
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 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 
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 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
] 
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[1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133]
[1134] [1135] [1136]
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1137] [1138]
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1139] [1140] [1141]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/pcr/m/n/10 where =
[1142] [1143]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[]
[][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
[1144] [1145] [1146]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and
[1147]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1148] [1149] [1150]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1151] [1152] [1153] [1154] [1155] [1156] [1157]
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[]\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu
rns the im-plicit generic ver-sion,
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\T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \
T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents
[1158] [1159]
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1160]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
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[]
[1161] [1162]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =
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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1163]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =
Underfull \hbox (badness 6157) in paragraph at lines 3908--3912
[]\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/
ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
[1164] [1165] [1166]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1167] [1168] [1169]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 
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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1170]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1171] [1172] [1173]
Underfull \hbox (badness 2126) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the 
im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 ,
[1174] [1175] [1176]
Underfull \hbox (badness 10000) in paragraph at lines 4811--4820
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1177] [1178] [1179] [1180]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1181]
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 
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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 
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[1183]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5356
[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1184] [1185]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1186] [1187] [1188]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1189] [1190] [1191] [1192] [1193] [1194]
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[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1195] [1196]
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,
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\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1197]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1198] [1199]
Underfull \hbox (badness 2875) in paragraph at lines 6647--6656
[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
Underfull \hbox (badness 1436) in paragraph at lines 6647--6656
[][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten 
a good idea; they will be called by call-ing
[1200]
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[1202] [1203]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1204]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1205] [1206]
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 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 
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 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1208]
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[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3209) in paragraph at lines 7309--7321
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1209] [1210]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
Underfull \hbox (badness 10000) in paragraph at lines 7496--7499
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1211]
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 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[] 
[1212]
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\T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re-
sult to be from some class
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223]
Underfull \hbox (badness 1052) in paragraph at lines 8489--8496
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1224]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1225]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1226] [1227] [1228] [1229]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1230] [1231] [1232]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1233] [1234] [1235]
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 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1236] [1237] [1238] [1239]
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 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1240]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250]
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
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\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1251] [1252] [1253]) (./parallel-pkg.tex [1254]
Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1255]
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[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1256] [1257]
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[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1258]
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, 
So-laris and Win-dows.
[1259] [1260]
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1261] [1262] [1263] [1264] [1265]
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[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class
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\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1266] [1267]
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 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1268] [1269] [1270]
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 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1271]
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[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1272]
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[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if
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 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1273] [1274]
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 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 
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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1275]
Underfull \hbox (badness 1577) in paragraph at lines 1401--1404
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1448--1450
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1276] [1277]) (./splines-pkg.tex [1278]
Chapter 9.
Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286]
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 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1287]
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[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object)
 -1 \T1/ptm/m/n/10 spec-i-fy-ing the
[1288] [1289]
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 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1290] [1291] [1292]) (./stats-pkg.tex
Chapter 10.
[1293]
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[]\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o
f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
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 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 
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 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
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 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1299]
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
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\T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r
or strata of class
Underfull \hbox (badness 2343) in paragraph at lines 1544--1548
\T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T
1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T
1/ptm/m/n/10 meth-ods avail-able for
[1316]
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 []          \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm 
= TRUE)[] 
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 []          \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm 
= TRUE)[] 
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 []                 \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[] 
[1319]
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 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
 specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
] 
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[1331] [1332] [1333]
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 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1334] [1335] [1336] [1337]
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 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1338] [1339] [1340]
Underfull \hbox (badness 10000) in paragraph at lines 3251--3253
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1341]
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 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
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 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1342] [1343] [1344] [1345] [1346]
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 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1347] [1348] [1349] [1350]
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 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1351] [1352] [1353] [1354] [1355]
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 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
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 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1356] [1357] [1358] [1359]
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 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1360] [1361]
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 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1362] [1363]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1364] [1365] [1366] [1367] [1368]
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 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 
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 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1369] [1370] [1371]
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 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 
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 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1372]
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[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1373] [1374] [1375]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
Underfull \hbox (badness 1448) in paragraph at lines 5606--5611
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1376] [1377]
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 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1378] [1379] [1380]
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 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1381] [1382] [1383]
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 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1384] [1385]
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 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1386]
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[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T
1/pcr/m/n/10 y
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1390]
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[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method
Underfull \hbox (badness 5563) in paragraph at lines 6618--6620
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6621--6626
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
[1391]
Underfull \hbox (badness 7238) in paragraph at lines 6657--6660
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
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 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str =  "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[] 
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 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
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 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
[1392]
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 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1393] [1394] [1395]
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 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
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[1397] [1398]
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[1400] [1401] [1402]
Underfull \hbox (badness 10000) in paragraph at lines 7366--7370
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1403]
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1404] [1405]
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1406] [1407] [1408] [1409] [1410] [1411]
Underfull \hbox (badness 10000) in paragraph at lines 8014--8019
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1412] [1413] [1414] [1415] [1416] [1417]
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[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1418] [1419] [1420] [1421] [1422] [1423]
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 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 
[1424]
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 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 
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 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1425] [1426]
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 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1427] [1428] [1429] [1430] [1431] [1432]
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 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 
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 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1433] [1434] [1435]
Underfull \hbox (badness 7291) in paragraph at lines 9625--9627
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1436] [1437] [1438] [1439] [1440] [1441] [1442]
Underfull \hbox (badness 6944) in paragraph at lines 10103--10109
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1443] [1444] [1445]
Underfull \hbox (badness 3758) in paragraph at lines 10317--10320
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1446] [1447] [1448] [1449]
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 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1450]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
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[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T
1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1451]
Underfull \hbox (badness 10000) in paragraph at lines 10731--10734
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1452] [1453] [1454]
Underfull \hbox (badness 2142) in paragraph at lines 10948--10951
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1455]
Underfull \hbox (badness 1708) in paragraph at lines 11029--11033
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1456]
Underfull \hbox (badness 10000) in paragraph at lines 11071--11077
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11109--11114
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1457] [1458]
Underfull \hbox (badness 2635) in paragraph at lines 11242--11245
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1459] [1460] [1461]
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1462]
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 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1463]
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 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
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[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1464] [1465] [1466] [1467] [1468]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11894--11894
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1469]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11909 \aliasA{hat}{influence.measures}{hat}
                                             
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 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1470]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11981--11981
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
Underfull \hbox (badness 1062) in paragraph at lines 12034--12039
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12051--12053
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1471] [1472] [1473] [1474]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12305--12305
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12306--12306
 []                 \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[] 
[1475] [1476] [1477] [1478] [1479] [1480]
Underfull \hbox (badness 10000) in paragraph at lines 12650--12652
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12673--12675
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
[1481]
Underfull \hbox (badness 2753) in paragraph at lines 12742--12744
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1482] [1483] [1484] [1485]
Underfull \hbox (badness 6910) in paragraph at lines 12980--12982
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of \T1/pcr/m/n/10 ob
Underfull \hbox (badness 2894) in paragraph at lines 12986--12990
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 12986--12990
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13592--13592
 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[] 
[1495]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13693--13693
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1496]
Underfull \hbox (badness 4518) in paragraph at lines 13737--13742
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1497] [1498] [1499]
Underfull \hbox (badness 10000) in paragraph at lines 13936--13940
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1500] [1501] [1502] [1503] [1504]
Underfull \hbox (badness 1163) in paragraph at lines 14270--14278
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1505]
Underfull \hbox (badness 4518) in paragraph at lines 14390--14395
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14578--14578
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14579--14579
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1509] [1510] [1511] [1512] [1513]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14922--14922
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14923--14923
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1514] [1515]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 15016--15016
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1516] [1517] [1518] [1519] [1520] [1521]
Underfull \hbox (badness 2726) in paragraph at lines 15422--15425
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1522]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15516--15516
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 16142--16142
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1533] [1534]
Underfull \hbox (badness 1490) in paragraph at lines 16280--16285
\T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are
 re-cy-cled to the num-ber of data frame rows. Un-like
[1535]
Underfull \hbox (badness 1648) in paragraph at lines 16346--16348
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
Underfull \hbox (badness 2591) in paragraph at lines 16361--16370
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would
Underfull \hbox (badness 3930) in paragraph at lines 16361--16370
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1536]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16431--16431
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16432--16432
 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[] 
[1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16989--16989
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1546] [1547] [1548]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17221--17221
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558]
Underfull \vbox (badness 10000) has occurred while \output is active [1559]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 17943--17943
 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
 
Underfull \vbox (badness 10000) has occurred while \output is active [1560]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17961--17961
 []\T1/pcr/m/n/9 ## Here, requiring close convergence, you need to use more acc
urate numerical[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 17962--17962
 []\T1/pcr/m/n/9 ##  differentiation; this gives Error: "step factor .. reduced
 below \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ..
"[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 17965--17965
 []\T1/pcr/m/n/9 try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where
 central diff. work here:[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 17966--17966
 []   \T1/pcr/m/n/9 (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral
=TRUE), trace=TRUE))[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17998--17998
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1561] [1562] [1563]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18174--18174
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1564]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18221--18221
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18268--18268
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1565] [1566] [1567] [1568]
Overfull \hbox (102.78088pt too wide) in paragraph at lines 18474--18474
 []             \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[] 
[1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 1248) in paragraph at lines 18789--18792
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 18802--18806
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 18810--18814
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and
[1574]
Underfull \hbox (badness 2042) in paragraph at lines 18868--18870
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1575]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18974--18974
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
[1576]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19017--19017
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19035--19035
 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19038--19038
 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19058--19058
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
[1577]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19061--19061
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
Underfull \hbox (badness 2564) in paragraph at lines 19096--19107
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19096--19107
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1578]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19159--19159
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1579] [1580] [1581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19386--19386
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1582] [1583]
Underfull \hbox (badness 1337) in paragraph at lines 19497--19500
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1584] [1585] [1586] [1587] [1588]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19816--19816
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1589] [1590]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19904--19904
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 19906--19906
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 19908--19908
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1591]
Underfull \hbox (badness 10000) in paragraph at lines 19954--19960
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/
pcr/m/n/10 iter \T1/ptm/m/n/10 in
Underfull \hbox (badness 3049) in paragraph at lines 19995--19999
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1592] [1593] [1594] [1595]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20248--20248
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 1194) in paragraph at lines 20258--20261
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1596]
Underfull \hbox (badness 1107) in paragraph at lines 20316--20318
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1597]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20371--20371
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1598]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20378--20378
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 
[1599]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20472--20472
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1600] [1601]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20601--20601
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1602]
Underfull \hbox (badness 7740) in paragraph at lines 20664--20666
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of
[1603]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20712--20712
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1604]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20804--20804
 [] \T1/pcr/m/n/9 zm <- zapsmall(polym (    1:4, c(1, 4:6),  degree = 3)) # or 
just poly():[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 20809--20809
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615]
[1616] [1617]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 21664--21664
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[] 
[1618]
Underfull \hbox (badness 6859) in paragraph at lines 21731--21738
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 21742--21748
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629]
[1630]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22488--22488
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1631] [1632] [1633] [1634] [1635]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22772--22772
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22773--22773
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1636] [1637] [1638] [1639] [1640]
Underfull \hbox (badness 1337) in paragraph at lines 23099--23105
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1641] [1642] [1643] [1644] [1645] [1646] [1647]
Underfull \hbox (badness 2913) in paragraph at lines 23524--23527
[]\T1/ptm/m/n/10 used only when \T1/pcr/m/n/10 names \T1/ptm/m/n/10 is true: th
e pre-ci-sion to use when for-mat-
Underfull \hbox (badness 1152) in paragraph at lines 23524--23527
\T1/ptm/m/n/10 ting the per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-s
ions up to 4.0.x, this had been set to
[1648]
Underfull \hbox (badness 10000) in paragraph at lines 23658--23660
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 23658--23660
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 23665--23666
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1649] [1650]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 23776--23776
 []       \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[] 
[1651]
Underfull \hbox (badness 1028) in paragraph at lines 23834--23837
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1652] [1653]
Underfull \hbox (badness 10000) in paragraph at lines 23949--23952
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 7944) in paragraph at lines 24004--24006
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1654]
Underfull \hbox (badness 7944) in paragraph at lines 24066--24068
[]\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is
 a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels =
[1655] [1656]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24168--24168
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1657] [1658]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24285--24285
 []\T1/pcr/m/n/10 #         varying = ___,  # list / matrix / vector (use with 
care)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24286--24286
 []\T1/pcr/m/n/10 #         v.names = ___,  # vector of variable names in long 
format[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24287--24287
 []\T1/pcr/m/n/10 #         timevar, times, # name / values of constructed time
 variable[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24288--24288
 []\T1/pcr/m/n/10 #         idvar, ids)     # name / values of constructed id v
ariable[] 
[1659] [1660]
Underfull \hbox (badness 10000) in paragraph at lines 24448--24453
[][][]\T1/pcr/m/n/10 stack[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 aperm[][][]
\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 relist[][][] \T1/ptm/m/n/10 for re-shap-ing
 the re-sult of [][]\T1/pcr/m/n/10 unlist[][][]\T1/ptm/m/n/10 . [][]\T1/pcr/m/n
/10 xtabs[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 24448--24453
[][]\T1/pcr/m/n/10 as.data.frame.table[][][] \T1/ptm/m/n/10 for cre-at-ing con-
tin-gency ta-bles and con-vert-ing them back to
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24459--24459
 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24460--24460
 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[] 
[1661]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24479--24479
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1662]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 24583--24583
 []       \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[] 
[1663]
Underfull \hbox (badness 1033) in paragraph at lines 24626--24632
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
Underfull \hbox (badness 10000) in paragraph at lines 24647--24650
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] =
[1664]
Underfull \hbox (badness 2134) in paragraph at lines 24716--24720
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24729--24729
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1665]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24758--24758
 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
 used to fail badly (notably for "Turlach"):[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[] 
[1666] [1667] [1668] [1669] [1670] [1671] [1672]
Underfull \hbox (badness 6268) in paragraph at lines 25228--25233
[][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
SSmicmen[][][]\T1/ptm/m/n/10 ,
[1673]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 25256--25256
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1674] [1675] [1676]
Underfull \hbox (badness 1867) in paragraph at lines 25433--25435
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 25448--25452
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback =
 use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 25448--25452
\T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in
 older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25484--25484
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25491--25491
 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[] 
[1677] [1678] [1679]
Underfull \hbox (badness 2495) in paragraph at lines 25674--25683
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1680]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25756--25756
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
[1681]
Underfull \hbox (badness 1412) in paragraph at lines 25763--25765
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1682]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25850--25850
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25875--25875
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25878--25878
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1683] [1684] [1685]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26102--26102
 []    \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[] 
Underfull \hbox (badness 2547) in paragraph at lines 26106--26112
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a
nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only
[1686]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26152--26152
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26173--26173
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1687]
Underfull \hbox (badness 1019) in paragraph at lines 26235--26240
\T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow
 \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value
[1688] [1689]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 26365--26365
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1690] [1691] [1692] [1693] [1694] [1695]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26745--26745
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1696] [1697]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26926--26926
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 
[1698]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 26932--26932
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))  
for when x has ties")[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26941--26941
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26942--26942
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
[1699]
Underfull \hbox (badness 2922) in paragraph at lines 27011--27016
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27048--27048
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
[1700]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27051--27051
 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27060--27060
 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27061--27061
 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27065--27065
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1701]
Underfull \hbox (badness 3240) in paragraph at lines 27119--27122
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27140--27140
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27143--27143
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1702]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27226--27226
 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27230--27230
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
[1703]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 27240--27240
 []  \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), 
phi[1]), pos=0, las=1)[] 
Overfull \hbox (106.98032pt too wide) in paragraph at lines 27245--27245
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
Underfull \hbox (badness 2922) in paragraph at lines 27281--27287
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27303--27303
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27319--27319
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27335--27335
 []        \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[] 
Overfull \hbox (128.58029pt too wide) in paragraph at lines 27338--27338
 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, control = list(scaleOffset=1))[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 27340--27340
 []           \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1
e-11, nDcentral=TRUE), trace=TRUE)[] 
[1705] [1706]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 27452--27452
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1707]
Underfull \hbox (badness 2922) in paragraph at lines 27514--27519
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1708]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27552--27552
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
Underfull \hbox (badness 2922) in paragraph at lines 27601--27606
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1709]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27632--27632
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
Underfull \hbox (badness 2922) in paragraph at lines 27666--27671
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27691--27691
 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27695--27695
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27715--27715
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
[1711]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27725--27725
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 
Underfull \hbox (badness 2922) in paragraph at lines 27760--27765
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27782--27782
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
[1712]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27800--27800
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1713]
Underfull \hbox (badness 6493) in paragraph at lines 27852--27857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27880--27880
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27883--27883
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 27886--27886
 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27889--27889
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724]
[1725] [1726] [1727]
Underfull \hbox (badness 3396) in paragraph at lines 28772--28774
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1728] [1729]
Underfull \hbox (badness 2237) in paragraph at lines 28949--28951
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1730] [1731] [1732]
Underfull \hbox (badness 2591) in paragraph at lines 29113--29115
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1733]
Underfull \hbox (badness 2237) in paragraph at lines 29159--29162
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1734]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 29232--29232
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1735]
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[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
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en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
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[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i
-tive nu-meric tol-er-ance, used in
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 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] 
[1783] [1784]) (./stats4-pkg.tex
Chapter 11.
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Chapter 12.
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whose
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Chapter 13.
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
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m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
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1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
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\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1127) in paragraph at lines 4815--4821
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 4815--4821
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
[1889]
Underfull \hbox (badness 1571) in paragraph at lines 4843--4847
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
Underfull \hbox (badness 2772) in paragraph at lines 4869--4874
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\
T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing
 ex-ist-ing
[1890] [1891] [1892]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1893] [1894] [1895] [1896]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 258--258
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1897]
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\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1898]
Underfull \hbox (badness 10000) in paragraph at lines 384--386
[]\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han-
dles, by de-fault pro-duced by
[1899]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450
 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 452--452
 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469
 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1900] [1901] [1902]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 677--677
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
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 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 684--684
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 685--685
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 686--686
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 
Underfull \hbox (badness 10000) in paragraph at lines 720--726
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 720--726
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1903] [1904]
Underfull \hbox (badness 4505) in paragraph at lines 857--863
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1905] [1906] [1907]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1043--1043
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1908]
Underfull \hbox (badness 1748) in paragraph at lines 1108--1116
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10
 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/
ptm/m/n/10 , in-di-cat-
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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-
Underfull \hbox (badness 1661) in paragraph at lines 1108--1116
\T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \
T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally.
Underfull \hbox (badness 1817) in paragraph at lines 1108--1116
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1909]
Underfull \hbox (badness 10000) in paragraph at lines 1228--1231
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1910] [1911]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1311--1311
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1912] [1913] [1914] [1915] [1916] [1917] [1918]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1813--1813
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1919]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1848--1848
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1920]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1994--1994
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1921]
Underfull \hbox (badness 10000) in paragraph at lines 2063--2068
[]\T1/pcr/m/n/10 charClass \T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/ptm
/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-
Underfull \hbox (badness 10000) in paragraph at lines 2063--2068
\T1/ptm/m/n/10 ac-ter classes which also worked in ear-lier ver-sions is to use
 some-thing like
[1922]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2096--2096
 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", 
"upper", "xdigit")[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2098--2098
 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106
 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
 Unicode 13.)[] 
[1923] [1924] [1925]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2254--2254
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1926]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2306--2306
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1927] [1928]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2475--2475
 []                 \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] 
[1929]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2498--2498
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2618--2618
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1931]
Underfull \hbox (badness 1082) in paragraph at lines 2692--2696
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2697 ... the Clipboard in MS Windows}{clipboard}
                                                   [1932]
Underfull \hbox (badness 1163) in paragraph at lines 2728--2730
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1933]
Underfull \hbox (badness 10000) in paragraph at lines 2816--2818
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1934] [1935] [1936] [1937]
Underfull \hbox (badness 10000) in paragraph at lines 3034--3036
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1938] [1939] [1940] [1941]
Underfull \hbox (badness 1762) in paragraph at lines 3328--3331
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1942]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3421--3421
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1943]
Underfull \hbox (badness 2452) in paragraph at lines 3497--3500
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1944] [1945] [1946] [1947] [1948] [1949]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3906--3906
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1950]
Underfull \hbox (badness 10000) in paragraph at lines 3990--3994
[]\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is 
op-tional on Win-dows: use
[1951]
Underfull \hbox (badness 1072) in paragraph at lines 4058--4066
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1952]
Underfull \hbox (badness 1231) in paragraph at lines 4135--4147
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 4149--4154
[]\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = 
"libcurl"\T1/ptm/m/n/10 , in-clud-ing
Underfull \hbox (badness 7595) in paragraph at lines 4149--4154
\T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1
0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents
 of
Underfull \hbox (badness 1331) in paragraph at lines 4149--4154
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1953] [1954]
Underfull \hbox (badness 4660) in paragraph at lines 4269--4272
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4293--4295
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1955] [1956] [1957]
Underfull \hbox (badness 1565) in paragraph at lines 4478--4482
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[1958]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4561--4561
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1959]
Underfull \hbox (badness 1931) in paragraph at lines 4596--4603
[]\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat
-ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[1960] [1961] [1962] [1963] [1964]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4920--4920
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1965]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4991 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4991 ...mat Unordered and Ordered Lists}{format}
                                                   [1966] [1967] [1968]
[1969] [1970] [1971] [1972] [1973]
Underfull \hbox (badness 1622) in paragraph at lines 5510--5514
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1974] [1975] [1976] [1977] [1978]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 5832--5832
 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 '  \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 5844--5844
 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported 
as tail.matrix()[] 
[1979] [1980]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5977--5977
 []    \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5978--5978
 []    \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops 
"other" attributes ..[] 
[1981] [1982] [1983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6188--6188
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1984]
Underfull \hbox (badness 10000) in paragraph at lines 6272--6274
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1985]
Underfull \hbox (badness 1502) in paragraph at lines 6321--6326
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
Underfull \hbox (badness 2103) in paragraph at lines 6321--6326
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1986] [1987]
Underfull \hbox (badness 10000) in paragraph at lines 6494--6503
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
Underfull \hbox (badness 10000) in paragraph at lines 6494--6503
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1988]
Underfull \hbox (badness 2150) in paragraph at lines 6558--6561
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
Underfull \hbox (badness 5175) in paragraph at lines 6574--6577
[]\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search 
database for sub-se-quent use by
[1989] [1990]
Underfull \hbox (badness 3118) in paragraph at lines 6697--6699
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1991] [1992]
Underfull \hbox (badness 5091) in paragraph at lines 6872--6874
[]\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
[1993]
Underfull \hbox (badness 5331) in paragraph at lines 6888--6894
[]\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa
ck-ages which
Underfull \hbox (badness 1137) in paragraph at lines 6888--6894
\T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re-
cur-sively).
Overfull \hbox (20.55087pt too wide) in paragraph at lines 6888--6894
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 
Overfull \hbox (30.30977pt too wide) in paragraph at lines 6902--6909
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I
mports","LinkingTo","Suggests")
Underfull \hbox (badness 1270) in paragraph at lines 6917--6927
\T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in
 the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If
[1994]
Underfull \hbox (badness 10000) in paragraph at lines 6960--6963
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be
Underfull \hbox (badness 10000) in paragraph at lines 6960--6963
\T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour
ce pack-age in-stall. E.g.,
Underfull \hbox (badness 1424) in paragraph at lines 6968--6971
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
[1995]
Underfull \hbox (badness 2376) in paragraph at lines 7039--7046
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1
0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7039--7046
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 7039--7046
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 7047--7050
[]\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/
n/10 al-ways works pro-vided the pack-age con-tains no
[1996]
Underfull \hbox (badness 1314) in paragraph at lines 7126--7133
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
Underfull \hbox (badness 10000) in paragraph at lines 7173--7176
[]\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing \T1/pcr/m/n/10 available.pac
kages(filters =
Underfull \hbox (badness 1314) in paragraph at lines 7173--7176
\T1/pcr/m/n/10 "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 ,] \T1/ptm/m/n/
10 will show if the pack-age is avail-able for any \T1/phv/m/n/10 R \T1/ptm/m/n
/10 ver-sion (for
Underfull \hbox (badness 10000) in paragraph at lines 7206--7211
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,
[1997]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7229--7229
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
Underfull \hbox (badness 5133) in paragraph at lines 7265--7269
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7279--7282
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1998]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7326--7326
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1999] [2000]
Underfull \hbox (badness 4132) in paragraph at lines 7450--7452
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[2001] [2002] [2003]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7617--7617
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[2004] [2005]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7760--7760
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[2006]
Underfull \hbox (badness 10000) in paragraph at lines 7800--7802
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2007] [2008]
Underfull \hbox (badness 10000) in paragraph at lines 7988--7990
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 7993--7995
[]\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n
/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class
[2009] [2010] [2011] [2012]
Underfull \hbox (badness 1859) in paragraph at lines 8221--8224
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[2013]
Underfull \hbox (badness 1655) in paragraph at lines 8315--8318
[]\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db"
\T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n
/10 (and
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8326--8326
 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8334--8334
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 
[2014]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8342--8342
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[2015]
Underfull \hbox (badness 1917) in paragraph at lines 8429--8431
[]\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 ,
[2016] [2017] [2018] [2019]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8701--8701
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 8702--8702
 []            \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[] 
Overfull \hbox (84.78088pt too wide) in paragraph at lines 8703--8703
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 8731--8733
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr
/m/n/10 character[][][] \T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 8745--8747
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like \T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 8753--8758
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
[2021]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8799--8799
 []          \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8800--8800
 []                                   \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] 
[2022] [2023]
Underfull \hbox (badness 10000) in paragraph at lines 8929--8934
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by
Underfull \hbox (badness 10000) in paragraph at lines 8929--8934
[][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
Underfull \hbox (badness 3635) in paragraph at lines 8929--8934
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion
Underfull \hbox (badness 10000) in paragraph at lines 8936--8939
\T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-
els \T1/pcr/m/n/10 c("installed","not
[2024]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9052--9052
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9053--9053
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[2025] [2026] [2027]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9226--9226
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[2028]
Underfull \hbox (badness 1789) in paragraph at lines 9359--9361
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037]
Underfull \hbox (badness 5203) in paragraph at lines 9932--9935
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[2038] [2039]
Underfull \hbox (badness 1394) in paragraph at lines 10158--10165
\T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc
r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10
 , try-ing to com-plete
[2040]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10182--10182
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[2041] [2042]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10343--10343
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2043] [2044] [2045]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10524--10524
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[2046]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10610--10610
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10613--10613
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10618--10618
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2047]
Underfull \hbox (badness 2027) in paragraph at lines 10690--10693
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[2048] [2049] [2050] [2051]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10962--10962
 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10963--10963
 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
Underfull \hbox (badness 10000) in paragraph at lines 10970--10975
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 10970--10975
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/
n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10970--10975
\T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2052] [2053] [2054]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11203--11203
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2055] [2056] [2057] [2058] [2059]
Underfull \hbox (badness 10000) in paragraph at lines 11464--11468
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11482--11482
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11487--11487
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2060] [2061]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11620--11620
 []\T1/pcr/m/n/10 4. |     \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 11621--11621
 []\T1/pcr/m/n/10 5. |       \-base:::doTryCatch(return(expr), name, parentenv,
 handler)[] 
[2062] [2063]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11756--11756
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2064]
Underfull \hbox (badness 1917) in paragraph at lines 11880--11883
[]\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u
sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari-
Underfull \hbox (badness 4328) in paragraph at lines 11880--11883
\T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If
 this is set, then it takes prece-dence over
[2065]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 11903--11903
 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] 
[2066]
Underfull \hbox (badness 10000) in paragraph at lines 11966--11968
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\
T1/ptm/m/n/10 s are nicely viewed via
[2067]
Underfull \hbox (badness 6725) in paragraph at lines 12016--12025
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-
Underfull \hbox (badness 10000) in paragraph at lines 12016--12025
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,
Underfull \hbox (badness 1997) in paragraph at lines 12016--12025
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[2068]
Underfull \hbox (badness 1377) in paragraph at lines 12116--12119
[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style (\T1/pcr/m/
n/10 "etags"\T1/ptm/m/n/10 ) or vi style
[2069]
Underfull \hbox (badness 3646) in paragraph at lines 12151--12153
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
Overfull \hbox (30.78088pt too wide) in paragraph at lines 12189--12189
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2070] [2071] [2072]
Underfull \hbox (badness 10000) in paragraph at lines 12370--12374
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able
Underfull \hbox (badness 10000) in paragraph at lines 12401--12407
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2073] [2074]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 12577--12577
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
[2075]
Underfull \hbox (badness 1009) in paragraph at lines 12595--12607
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
Underfull \hbox (badness 2600) in paragraph at lines 12635--12637
[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
 the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and
[2076]
Underfull \hbox (badness 1043) in paragraph at lines 12678--12683
[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
 con-fig-ured the map-ping of font num-bers to fonts, and
[2077] [2078] [2079] [2080]
Underfull \hbox (badness 1888) in paragraph at lines 12971--12974
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10
 R \T1/ptm/m/n/10 was built un-der. Where
Underfull \hbox (badness 10000) in paragraph at lines 12988--12991
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2081]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13034--13034
 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 
[2082]
Underfull \hbox (badness 2158) in paragraph at lines 13089--13092
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
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 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2083] [2084] [2085]
Underfull \hbox (badness 2302) in paragraph at lines 13294--13296
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2086]
Underfull \hbox (badness 3333) in paragraph at lines 13401--13403
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[2087] [2088] [2089]
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 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
Underfull \hbox (badness 2012) in paragraph at lines 13592--13597
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][
]\T1/pcr/m/n/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have
Underfull \hbox (badness 5970) in paragraph at lines 13601--13604
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
Underfull \hbox (badness 2600) in paragraph at lines 13601--13604
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2090]
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[]\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, 
de-ter-min-ing the \T1/pcr/m/n/10 nlines \T1/ptm/m/n/10 ar-gu-ment to
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13674--13674
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2091]
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 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13712--13712
 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13714--13714
 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2092]
[2093] [2094]
Underfull \hbox (badness 10000) in paragraph at lines 13882--13884
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[2095] [2096]
Underfull \hbox (badness 6300) in paragraph at lines 14039--14046
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 14039--14046
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[2097] [2098]
Underfull \hbox (badness 2020) in paragraph at lines 14208--14224
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 14208--14224
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2099] [2100]
Underfull \hbox (badness 5022) in paragraph at lines 14347--14351
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 14354--14357
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
[2101] [2102] [2103]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14518--14518
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2104] [2105] [2106] [2107] [2108] [2109]
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
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[]\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1
/ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 4660) in paragraph at lines 15001--15005
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =
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[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be
Underfull \hbox (badness 10000) in paragraph at lines 15021--15026
\T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15021--15026
\T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1
/ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][]
Underfull \hbox (badness 1052) in paragraph at lines 15027--15029
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2110]
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\T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av
ailable.packages(contriburl =
Underfull \hbox (badness 1509) in paragraph at lines 15057--15062
\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
 fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with
Underfull \hbox (badness 10000) in paragraph at lines 15086--15089
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[2111]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15140--15140
 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt") 
[2112] [2113] [2114]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Underfull \hbox (badness 1253) in paragraph at lines 15347--15350
[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2115]
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 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
 
[2116]
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 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
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 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2117] [2118]
Underfull \hbox (badness 1297) in paragraph at lines 15583--15585
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2119]
Underfull \hbox (badness 4036) in paragraph at lines 15630--15632
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de
lete a menu and all of its items and sub-menus.
[2120] [2121]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2122]
Underfull \hbox (badness 1715) in paragraph at lines 15819--15822
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 15864--15866
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/pcr/m/n/10 file =
[2123] [2124] [2125]) [2126] [2127] [2128] (./KernSmooth-pkg.tex
Chapter 15.
[2129]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2130] [2131] [2132] [2133] [2134]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2135] [2136] [2137] [2138]) (./MASS-pkg.tex
Chapter 16.
[2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160]
[2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171]
[2172]
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2173] [2174] [2175] [2176]
Underfull \hbox (badness 6559) in paragraph at lines 2703--2706
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[2177] [2178] [2179]
Underfull \hbox (badness 10000) in paragraph at lines 2873--2878
\T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt
m/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2873--2878
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1
/ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\
T1/ptm/m/n/10 ,
[2180] [2181]
Underfull \hbox (badness 4686) in paragraph at lines 3041--3043
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2182] [2183] [2184]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3236--3236
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2185]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196]
[2197]
Underfull \hbox (badness 1845) in paragraph at lines 4154--4156
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[2198] [2199] [2200] [2201] [2202] [2203] [2204]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4650--4650
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2205] [2206] [2207]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219] [2220] [2221]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5924--5924
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2222]
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 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2223] [2224]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6146 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6146 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2225] [2226]
Underfull \hbox (badness 1783) in paragraph at lines 6266--6270
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2227] [2228] [2229] [2230]
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 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2231]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2232] [2233] [2234] [2235] [2236] [2237]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7093--7093
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7110--7110
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2238]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat
Underfull \hbox (badness 3138) in paragraph at lines 7188--7194
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2239]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2240] [2241]
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\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2242] [2243]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7497--7497
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2244]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7562--7562
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2245] [2246] [2247] [2248] [2249] [2250]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2251] [2252]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8143--8147
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262] [2263]
[2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9527--9527
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2273]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1
/pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1158) in paragraph at lines 9654--9657
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2274]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9738--9738
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9741--9741
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285]
[2286] [2287]) (./Matrix-pkg.tex [2288]
Chapter 17.
Underfull \hbox (badness 10000) in paragraph at lines 41--44
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2289]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2290]
Underfull \hbox (badness 2229) in paragraph at lines 159--162
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2291]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2292] [2293]
Underfull \hbox (badness 5147) in paragraph at lines 496--499
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2294]
Underfull \hbox (badness 5119) in paragraph at lines 509--513
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
Underfull \hbox (badness 1668) in paragraph at lines 513--518
[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Overfull \hbox (4.38043pt too wide) in paragraph at lines 543--543
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 545--545
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 
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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2295] [2296]
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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many*  (k x k) matrices:[] 
Overfull \hbox (96.18033pt too wide) in paragraph at lines 669--669
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  where each mat_j is a  k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 matrix\TS1/pcr/m/n/9 '[] 
Overfull \hbox (52.98038pt too wide) in paragraph at lines 670--670
 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) 
matrix of class  \code{"\linkS4class{dgCMatrix}"}.[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 683--683
 []        \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 684--684
 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 
[2297]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 689--689
 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 758--762
\T1/pcr/m/n/10 lapack / double / dsytrf . f$[][] \T1/ptm/m/n/10 and [][]$\T1/pc
r/m/n/10 https : / / www . netlib . org / lapack / double /
[2298] [2299]
Underfull \hbox (badness 3536) in paragraph at lines 877--882
[]\T1/ptm/m/n/10 option [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 in-di-c
at-ing if the re-sult should be sparse, i.e., for-
Underfull \hbox (badness 7777) in paragraph at lines 877--882
\T1/ptm/m/n/10 mally in-her-it-ing from \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"
\T1/ptm/m/n/10 . The de-fault, [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , de-
Underfull \hbox (badness 6188) in paragraph at lines 877--882
\T1/ptm/m/n/10 cides from the ``spar-sity'' of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n
/10 code in
[2300]
Underfull \hbox (badness 10000) in paragraph at lines 920--925
[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing \T1/pcr/m/n/10
 cbind2() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 rbind2() \T1/ptm/m/n/10 meth-ods:
[2301]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2302] [2303]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1168 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1168 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2304]
Underfull \hbox (badness 2285) in paragraph at lines 1254--1259
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2305]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2306]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
Underfull \hbox (badness 2277) in paragraph at lines 1423--1426
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2307]
Underfull \hbox (badness 1609) in paragraph at lines 1470--1474
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1497--1497
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1511--1511
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 
[2308]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1519--1519
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
Underfull \hbox (badness 10000) in paragraph at lines 1566--1573
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 5316) in paragraph at lines 1566--1573
\T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls 
of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or
[2309]
Underfull \hbox (badness 1783) in paragraph at lines 1601--1605
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
Underfull \hbox (badness 1221) in paragraph at lines 1617--1623
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1658 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1658 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1659 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1680 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1691 \aliasA{rowSums}{colSums}{rowSums}
                                          [2310]
Underfull \hbox (badness 2922) in paragraph at lines 1745--1749
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 1745--1749
\T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only
 ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a
Underfull \hbox (badness 1237) in paragraph at lines 1756--1759
[][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1
/pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 
v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since
[2311] [2312] [2313]
Underfull \hbox (badness 3547) in paragraph at lines 1910--1913
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2314] [2315] [2316] [2317]
Underfull \hbox (badness 1484) in paragraph at lines 2272--2274
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2318]
Underfull \hbox (badness 7379) in paragraph at lines 2368--2370
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2319] [2320] [2321]
Underfull \hbox (badness 4846) in paragraph at lines 2644--2648
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 2649--2653
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
 more than one pos-si-ble
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[]\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the
 su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\
T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ;
[2322]
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 []    \T1/pcr/m/n/10 .trDiagonal(n, x = 1,            uplo = "U", unitri=TRUE,
 kind)[] 
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[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
Underfull \hbox (badness 10000) in paragraph at lines 2716--2721
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10
 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse
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[][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 
triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo
[2323]
Underfull \hbox (badness 1097) in paragraph at lines 2739--2742
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
Underfull \hbox (badness 1142) in paragraph at lines 2752--2757
[][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de
-pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm
/m/n/10 ) rep-re-sen-ta-tion of
[2324]
Underfull \hbox (badness 3646) in paragraph at lines 2991--2994
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 10000) in paragraph at lines 3023--3025
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
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[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
Underfull \hbox (badness 5652) in paragraph at lines 3035--3041
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2325]
Underfull \hbox (badness 10000) in paragraph at lines 3042--3046
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3052--3056
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2326] [2327]
Underfull \hbox (badness 10000) in paragraph at lines 3236--3238
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3283--3285
[][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref
er-able to (and more ef-fi-cient than)
[2328]
Underfull \hbox (badness 2469) in paragraph at lines 3403--3406
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2329] [2330]
Underfull \hbox (badness 10000) in paragraph at lines 3568--3572
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",...) \T1/ptm/m/n/10 or
Underfull \hbox (badness 3815) in paragraph at lines 3568--3572
\T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e.
g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 ,
[2331]
Underfull \hbox (badness 2285) in paragraph at lines 3618--3621
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2332] [2333]
Underfull \hbox (badness 10000) in paragraph at lines 3765--3770
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by
Underfull \hbox (badness 6961) in paragraph at lines 3765--3770
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class
Underfull \hbox (badness 2608) in paragraph at lines 3777--3780
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2334]
Underfull \hbox (badness 10000) in paragraph at lines 3853--3855
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsyMatrix",...) \T1/ptm/m/n/10 or
[2335] [2336] [2337]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4064--4064
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
Underfull \hbox (badness 3635) in paragraph at lines 4132--4136
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class
[2338]
Underfull \hbox (badness 10000) in paragraph at lines 4141--4144
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
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\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
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[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2339] [2340]
Underfull \hbox (badness 3158) in paragraph at lines 4329--4333
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2341] [2342] [2343] [2344]
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 []\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe
ll-Boeing/counterx/counterx.html[] 
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 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB
/Boeing/msc00726.tar.gz"))))[] 
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 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 
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 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
 the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] 
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 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2345] [2346] [2347] [2348]
Underfull \hbox (badness 10000) in paragraph at lines 4889--4894
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2349]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4970--4970
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 
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 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4976--4976
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4983--4983
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2350] [2351]
Underfull \hbox (badness 4120) in paragraph at lines 5127--5130
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
[2352]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5164--5164
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
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 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,    
    border.col=NA)[] 
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 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[] 
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 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
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 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5184--5184
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 
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 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2353]
Underfull \hbox (badness 1817) in paragraph at lines 5276--5285
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the
[2354]
Underfull \hbox (badness 10000) in paragraph at lines 5318--5320
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T
his en-ables typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
Underfull \hbox (badness 4765) in paragraph at lines 5351--5354
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2355] [2356] [2357] [2358] [2359]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5669--5669
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
Underfull \hbox (badness 10000) in paragraph at lines 5752--5755
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5763--5763
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2360]
Underfull \hbox (badness 1622) in paragraph at lines 5800--5805
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),
Underfull \hbox (badness 1418) in paragraph at lines 5800--5805
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2361]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5862--5862
 []          \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5869--5869
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2362] [2363]
Underfull \hbox (badness 1062) in paragraph at lines 5998--6001
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 6027--6030
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2364]
Underfull \hbox (badness 2635) in paragraph at lines 6139--6144
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 6139--6144
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
[2365]
Underfull \hbox (badness 10000) in paragraph at lines 6147--6150
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
Underfull \hbox (badness 10000) in paragraph at lines 6257--6267
\T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/
n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 6257--6267
[][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/
10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p
cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 --
in
[2366]
Underfull \hbox (badness 3179) in paragraph at lines 6339--6342
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2367]
Underfull \hbox (badness 10000) in paragraph at lines 6437--6440
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2368]
Underfull \hbox (badness 10000) in paragraph at lines 6512--6515
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2369]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6528--6528
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
Underfull \hbox (badness 2443) in paragraph at lines 6567--6573
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see
Underfull \hbox (badness 1776) in paragraph at lines 6567--6573
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
Underfull \hbox (badness 1675) in paragraph at lines 6588--6591
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use
[2370]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6658--6658
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2371] [2372]
Underfull \hbox (badness 10000) in paragraph at lines 6799--6802
[]\T1/ptm/m/n/10 vector of all non-zero en-tries of \T1/pcr/m/n/10 x\T1/ptm/m/n
/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when
[2373]
Underfull \hbox (badness 1490) in paragraph at lines 6821--6823
[]\T1/pcr/m/n/10 mat2triplet() \T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/m/
it/10 in-verse \T1/ptm/m/n/10 func-tion of [][]\T1/pcr/m/n/10 spMatrix[][][] \T
1/ptm/m/n/10 and (one case of)
[2374]
Underfull \hbox (badness 5036) in paragraph at lines 6901--6905
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,
Underfull \hbox (badness 10000) in paragraph at lines 6901--6905
\T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em
pty'' [][]sparse-Ma-trix[][][], as does
[2375]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7000 \aliasA{det}{Matrix-class}{det}
                                       [2376]
Underfull \hbox (badness 10000) in paragraph at lines 7103--7106
Underfull \hbox (badness 10000) in paragraph at lines 7113--7115
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2377]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7176 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.7284 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.7383 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7480--7486
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2378]
Underfull \hbox (badness 10000) in paragraph at lines 7553--7556
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 1199) in paragraph at lines 7553--7556
\T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc
r/m/n/10 showMethods("%*%",class =
Underfull \hbox (badness 10000) in paragraph at lines 7556--7561
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use
Underfull \hbox (badness 1371) in paragraph at lines 7556--7561
\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-
Underfull \hbox (badness 1502) in paragraph at lines 7561--7565
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other
Underfull \hbox (badness 10000) in paragraph at lines 7561--7565
\T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class =
 "dgeMatrix")\T1/ptm/m/n/10 , ma-trix
Underfull \hbox (badness 2837) in paragraph at lines 7571--7572
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2379] [2380]
Underfull \hbox (badness 1009) in paragraph at lines 7707--7709
[]\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv
e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for
 $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see
[2381]
Underfull \hbox (badness 1062) in paragraph at lines 7752--7755
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
Underfull \hbox (badness 6063) in paragraph at lines 7786--7789
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2382]
Underfull \hbox (badness 10000) in paragraph at lines 7842--7844
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p
tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X
[2383] [2384]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 7944--7944
 []   \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7984--7984
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2385]
Underfull \hbox (badness 2635) in paragraph at lines 8049--8054
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 8049--8054
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 8057--8060
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2386]
Underfull \hbox (badness 3482) in paragraph at lines 8131--8137
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2387]
Underfull \hbox (badness 1867) in paragraph at lines 8251--8253
[]\T1/ptm/m/n/10 fast sim-
[2388]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8291 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.8291 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2389]
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 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379
 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8380--8380
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Underfull \hbox (badness 2401) in paragraph at lines 8493--8503
[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1
0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p
tm/m/n/10 ,
[2390]
Underfull \hbox (badness 3179) in paragraph at lines 8564--8567
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2391]
Underfull \hbox (badness 10000) in paragraph at lines 8654--8657
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 8730--8733
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2393]
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 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
Overfull \vbox (41.60564pt too high) has occurred while \output is active
[2394]
Underfull \hbox (badness 10000) in paragraph at lines 8856--8858
[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use
Underfull \hbox (badness 6493) in paragraph at lines 8858--8861
[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal
Underfull \hbox (badness 6428) in paragraph at lines 8864--8871
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2395] [2396]
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 
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 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8962--8962
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 8966--8966
 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 
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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
Underfull \hbox (badness 3989) in paragraph at lines 8992--9002
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 8992--9002
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2397] [2398]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9093 \aliasA{qr}{qr-methods}{qr}
                                   [2399]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9166--9166
 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed 
X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] 
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 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 
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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
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 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 
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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of
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[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2401] [2402]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9378--9378
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 
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 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol 
= 1e-7)) # all 14[] 
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
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 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9419 ... the Reciprocal Condition Number}{rcond}
                                                   [2403] [2404]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2405] [2406] [2407]
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional
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\T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n
row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is
 not
[2408] [2409]
Underfull \hbox (badness 1558) in paragraph at lines 9870--9873
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2410]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 
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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2411]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9998 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 
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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2412]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a
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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (
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\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
 if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric,
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2413]
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[]\T1/ptm/m/n/10 works via
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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use
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[]\T1/ptm/m/n/10 all work via
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[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and
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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2414]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)
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\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2415]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Underfull \hbox (badness 1158) in paragraph at lines 10375--10381
[]\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE)
 \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may
 be of-
[2416]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2417] [2418]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
[2419]
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[][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 string, one of \T1/pcr/m/n/
10 "C"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "T"\T1/ptm/m/n/10 , or \T1/pcr/m/n/10 "R"
\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
[2420]
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 
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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 
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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
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 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
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 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2421]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
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 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
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 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 
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 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 
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 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
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[2423]
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha
s been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11007 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2424] [2425]
Underfull \hbox (badness 10000) in paragraph at lines 11137--11139
[]\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc
r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 11165--11165
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2426]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-
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\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,
[2427]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2428]
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[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 11433--11435
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2429] [2430]
Underfull \hbox (badness 2698) in paragraph at lines 11558--11564
[][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us
ual con-struc-tor of such ma-tri-ces. Then,
[2431]
Underfull \hbox (badness 10000) in paragraph at lines 11651--11653
[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many
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[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/
n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
Underfull \hbox (badness 2050) in paragraph at lines 11669--11674
\T1/pcr/m/n/10 list(NULL,<character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H
ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
[2432]
Underfull \hbox (badness 2591) in paragraph at lines 11677--11682
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
Underfull \hbox (badness 2057) in paragraph at lines 11749--11751
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2433] [2434]
Underfull \hbox (badness 6641) in paragraph at lines 11835--11838
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in
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\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2435] [2436]
Underfull \hbox (badness 7649) in paragraph at lines 11982--11984
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2437] [2438] [2439]
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[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 
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 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2440] [2441] [2442]
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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 
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 []   \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/
x))$modulus))[] 
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 []   \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/
x))$modulus))[] 
[2443]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2444]
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref)                removing `\Rpercent' on input line 12605.
Package hyperref Warning: Glyph not defined in PU encoding,
(hyperref)                removing `\Rpercent' on input line 12605.
[2445] [2446]) (./boot-pkg.tex
Chapter 18.
[2447] [2448] [2449] [2450] [2451] [2452] [2453]
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 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2454]
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[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2455] [2456] [2457]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
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[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2458]
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 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
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[2460]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
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\T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply 
\T1/pcr/m/n/10 "all"
[2461]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
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\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2462] [2463] [2464] [2465]
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[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2466] [2467] [2468] [2469] [2470]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2471] [2472] [2473]
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 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2475]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2476] [2477] [2478]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2479]
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\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2440--2441
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2480] [2481]
Underfull \hbox (badness 1077) in paragraph at lines 2536--2540
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2536--2540
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2482] [2483] [2484] [2485] [2486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2487] [2488] [2489]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2490]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2491] [2492] [2493]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2494] [2495] [2496] [2497] [2498] [2499] [2500]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2501] [2502]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2503] [2504] [2505]
Underfull \hbox (badness 10000) in paragraph at lines 4190--4192
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2506]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2507] [2508]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4371--4375
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to
[2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2518] [2519] [2520] [2521]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2522]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2531]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2532]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2533] [2534] [2535] [2536]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2537] [2538]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2539] [2540] [2541]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2542] [2543]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2544] [2545] [2546] [2547] [2548] [2549] [2550] [2551]) (./class-pkg.tex
[2552]
Chapter 19.
[2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560] [2561] [2562] [2563]
[2564] [2565] [2566] [2567] [2568]) (./cluster-pkg.tex
Chapter 20.
[2569]
Underfull \hbox (badness 1655) in paragraph at lines 134--143
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly
Underfull \hbox (badness 2073) in paragraph at lines 134--143
\T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp
ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus-
Underfull \hbox (badness 1635) in paragraph at lines 134--143
\T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T
1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from
Underfull \hbox (badness 2134) in paragraph at lines 134--143
\T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1
/ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as
[2570] [2571]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 
Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2572] [2573]
Underfull \vbox (badness 10000) has occurred while \output is active [2574]
[2575]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2576] [2577]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2578]
Underfull \hbox (badness 3078) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2579] [2580]
Underfull \hbox (badness 2941) in paragraph at lines 791--794
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
[2581]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
Underfull \hbox (badness 10000) in paragraph at lines 881--883
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2582]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2583]
Underfull \hbox (badness 4872) in paragraph at lines 992--994
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 1006--1010
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2584] [2585]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1120--1120
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1137--1137
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2586]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1175--1175
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
Underfull \hbox (badness 4144) in paragraph at lines 1207--1211
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2587]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1283--1283
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1289--1289
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2588] [2589]
Underfull \hbox (badness 10000) in paragraph at lines 1428--1433
[]\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1
0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or
[2590]
Underfull \hbox (badness 10000) in paragraph at lines 1476--1479
Underfull \hbox (badness 10000) in paragraph at lines 1493--1497
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1517--1517
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1527--1527
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2591]
Underfull \hbox (badness 5741) in paragraph at lines 1567--1570
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2592]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2593] [2594]
Underfull \hbox (badness 1540) in paragraph at lines 1753--1761
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 =
[2595]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1844--1844
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1863--1863
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2596] [2597] [2598] [2599] [2600]
Underfull \hbox (badness 10000) in paragraph at lines 2182--2185
Underfull \hbox (badness 3179) in paragraph at lines 2196--2202
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2601] [2602]
Underfull \hbox (badness 10000) in paragraph at lines 2354--2357
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2603]
Underfull \hbox (badness 1292) in paragraph at lines 2422--2425
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2604]
Underfull \hbox (badness 6675) in paragraph at lines 2431--2433
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2454--2457
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2605] [2606] [2607]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2670--2670
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2608]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2749--2749
 []    \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[] 
[2609] [2610] [2611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2978--2978
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2612] [2613]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3081--3081
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2614] [2615] [2616]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2617]
Underfull \hbox (badness 10000) in paragraph at lines 3345--3348
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg
[2618]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3396--3396
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2619] [2620] [2621]
Underfull \hbox (badness 10000) in paragraph at lines 3581--3584
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for
[2622]
Underfull \hbox (badness 10000) in paragraph at lines 3644--3649
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2623]
Underfull \hbox (badness 3884) in paragraph at lines 3706--3711
\T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m
/n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx
Underfull \hbox (badness 6268) in paragraph at lines 3718--3721
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2624] [2625] [2626]
Underfull \hbox (badness 10000) in paragraph at lines 3903--3906
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 3934--3937
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2627]
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 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
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[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2628] [2629] [2630] [2631]
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 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 
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 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2632] [2633]
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 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 
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 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 
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 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 
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 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 
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 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
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 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2634] [2635] [2636] [2637] [2638] [2639] [2640]
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[]\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl
ightly more rounded than the one from
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[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
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 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 
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 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 
s medoid indices  == pam(xclara, 3)$id.med[] 
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 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2641]
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 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2642]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2643]
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[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2644]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2645] [2646] [2647]) (./foreign-pkg.tex [2648]
Chapter 22.
[2649]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
[2650] [2651]
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[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2652]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2653] [2654] [2655]
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 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2656]
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 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-
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\T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de-
fault), the first orig-i-nal value
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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,
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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
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\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli
cated_"\T1/ptm/m/n/10 ) if
[2657]
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / docs . microsoft . com / e
n-[]us / windows / win32 / intl /
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[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2658]
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 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 
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 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2659]
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 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 
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 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[] 
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 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2660] [2661]
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2662] [2663]
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 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2664]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
[2665] [2666]
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[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase 
/ format / data _ types .
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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2667] [2668]
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[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2669]
Underfull \hbox (badness 2088) in paragraph at lines 1296--1299
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef
-fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET
[2670]) (./lattice-pkg.tex
Chapter 23.
[2671]
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\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
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\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / 
ms / departments / sia /
[2672] [2673]
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2674]
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 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2675] [2676] [2677] [2678]
Underfull \hbox (badness 1221) in paragraph at lines 650--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2679] [2680] [2681] [2682]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2683]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2684] [2685]
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[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2686] [2687] [2688]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2689]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2690]
Underfull \vbox (badness 10000) has occurred while \output is active [2691]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2692]
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2693] [2694] [2695] [2696]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2697]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of
Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2698] [2699] [2700]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2701] [2702] [2703] [2704] [2705]
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 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2706] [2707]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2791--2796
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2708]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
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\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also
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[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from
[2709]
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[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2710]
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 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
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 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3106--3106
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
[2711]
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2712]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3187--3194
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2713] [2714] [2715]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3475 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                 [2716]
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2717] [2718] [2719] [2720] [2721]
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 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2722] [2723]
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2724]
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 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
[2725]
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
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\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2726]
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4214--4218
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2727] [2728]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4328--4338
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points
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\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and
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\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4356--4358
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2729] [2730] [2731] [2732] [2733]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2734] [2735]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2737] [2738]
Underfull \hbox (badness 1442) in paragraph at lines 5079--5082
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2739] [2740] [2741] [2742] [2743]
Underfull \hbox (badness 3646) in paragraph at lines 5413--5416
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or
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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 
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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2744]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
Underfull \hbox (badness 2103) in paragraph at lines 5532--5535
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing
[2745]
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[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2746] [2747]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 
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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5740--5740
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
[2748]
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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2749]
Underfull \hbox (badness 2538) in paragraph at lines 5894--5898
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 5905--5912
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 5905--5912
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2750] [2751]
Underfull \hbox (badness 10000) in paragraph at lines 6058--6062
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2752]
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[2754]
Underfull \hbox (badness 4242) in paragraph at lines 6205--6210
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2755] [2756]
Underfull \hbox (badness 3601) in paragraph at lines 6321--6326
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round
Underfull \hbox (badness 2486) in paragraph at lines 6321--6326
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2757]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2758] [2759]
Underfull \hbox (badness 1888) in paragraph at lines 6540--6547
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2760]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
Underfull \hbox (badness 1558) in paragraph at lines 6597--6600
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2761] [2762] [2763] [2764] [2765]
Underfull \hbox (badness 1320) in paragraph at lines 7003--7010
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-
Underfull \hbox (badness 1715) in paragraph at lines 7003--7010
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2766] [2767]
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to
Underfull \hbox (badness 1584) in paragraph at lines 7103--7107
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2768] [2769]
Underfull \hbox (badness 10000) in paragraph at lines 7208--7211
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2770] [2771]
Underfull \hbox (badness 2012) in paragraph at lines 7374--7377
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2772]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2773] [2774]
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to
Underfull \hbox (badness 2772) in paragraph at lines 7574--7577
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to
[2775]
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2776]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2777] [2778] [2779]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2780] [2781] [2782] [2783] [2784] [2785] [2786] [2787]
Underfull \hbox (badness 10000) in paragraph at lines 8518--8521
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
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\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2788] [2789]
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 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
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 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
[2790]
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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2791]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2792] [2793]
Underfull \hbox (badness 6316) in paragraph at lines 8907--8912
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2794]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2795] [2796]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9153--9153
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2797]
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[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,right,left.name,right.name,condition
Overfull \hbox (50.63074pt too wide) in paragraph at lines 9212--9216
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right
.x.name,right.y.name,condition
[2798] [2799] [2800] [2801] [2802] [2803] [2804]
Underfull \hbox (badness 7238) in paragraph at lines 9676--9680
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9676--9680
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,
[2805] [2806] [2807]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9907 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2808] [2809] [2810]
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\T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower
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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2811] [2812]) (./mgcv-pkg.tex
Chapter 24.
[2813] [2814]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 
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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2815]
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 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 377--384
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc
v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo
th.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 377--384
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 377--384
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2820]
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 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[] 
[2821] [2822] [2823]
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[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and
[2824] [2825]
Underfull \hbox (badness 1406) in paragraph at lines 702--703
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2826] [2827]
Underfull \hbox (badness 1158) in paragraph at lines 812--814
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2828]
Underfull \hbox (badness 1259) in paragraph at lines 875--876
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2829]
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[2831] [2832] [2833] [2834]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2835]
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 []    \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[] 
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[] 
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 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[] 
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 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
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 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
[2837]
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 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 
[2838]
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 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 
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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2848] [2849] [2850] [2851] [2852] [2853]
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\T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo
oths. Lin-ear func-tion-als of
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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 
Underfull \hbox (badness 1728) in paragraph at lines 2347--2350
[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1
0 formula.gam[][][] \T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2854]
Underfull \hbox (badness 1043) in paragraph at lines 2386--2391
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2855] [2856] [2857]
Underfull \hbox (badness 1043) in paragraph at lines 2551--2557
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2858]
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[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2687--2693
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2687--2693
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2859] [2860]
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[2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2871] [2872] [2873] [2874] [2875] [2876] [2877] [2878]
Underfull \hbox (badness 5189) in paragraph at lines 3821--3825
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2879] [2880]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3938--3938
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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[2882] [2883]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2884] [2885] [2886] [2887] [2888] [2889] [2890]
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 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2891] [2892] [2893]
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 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2894] [2895]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2896]
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[]\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc
e fail-ures, con-sider mod-i-fy-ing
[2897] [2898]
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[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1418) in paragraph at lines 5017--5023
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p
cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2899]
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[2901] [2902] [2903]
Underfull \hbox (badness 1577) in paragraph at lines 5369--5372
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5376--5377
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2904] [2905] [2906] [2907] [2908] [2909] [2910]
Underfull \hbox (badness 6708) in paragraph at lines 5765--5766
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(...,
fit=FALSE) \T1/ptm/m/n/10 or
[2911] [2912]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 5814--5814
 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5839--5839
 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 
[2913]
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 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 
[2914] [2915]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5990--5990
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2916] [2917] [2918] [2919] [2920]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
[2921]
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2922] [2923] [2924]
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[2926] [2927]
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 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2928] [2929] [2930] [2931]
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[2934] [2935]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944]
Underfull \hbox (badness 1242) in paragraph at lines 7668--7669
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2945] [2946]
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 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2947]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
[2948]
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
[2949] [2950] [2951] [2952] [2953] [2954] [2955] [2956] [2957] [2958] [2959]
[2960] [2961] [2962] [2963] [2964] [2965] [2966]
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Underfull \hbox (badness 10000) in paragraph at lines 9057--9060
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 9057--9060
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 9057--9060
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2968]
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[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 9113--9116
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2969] [2970] [2971] [2972]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 
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 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 
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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2973] [2974]
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\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2975] [2976]
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[2978]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2979]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/
10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para-
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\T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c
luded terms,
[2980] [2981]
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 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
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 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2987]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2988]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2989] [2990] [2991]
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[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2992] [2993] [2994] [2995] [2996]
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[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:
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\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2997]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 
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 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[] 
[2998]
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[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2999] [3000] [3001] [3002] [3003]
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 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL) 
[3004] [3005] [3006] [3007] [3008] [3009]
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 []  \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
 + (eps/del))[] 
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 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[] 
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[3011]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
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 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE,[] 
[3012]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n
/10 both.sides==FALSE \T1/ptm/m/n/10 then the re-
[3013] [3014] [3015]
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 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 
Underfull \hbox (badness 1975) in paragraph at lines 11851--11856
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3016]
Underfull \hbox (badness 1803) in paragraph at lines 11928--11932
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 11940--11952
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec
[3017]
Underfull \hbox (badness 2401) in paragraph at lines 11957--11961
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 11957--11961
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[3018] [3019] [3020]
Underfull \hbox (badness 6876) in paragraph at lines 12152--12158
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
[3021]
Underfull \hbox (badness 10000) in paragraph at lines 12193--12194
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3022] [3023]
Underfull \hbox (badness 10000) in paragraph at lines 12311--12312
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3024]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12365--12365
 []  \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12377--12377
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
[3025]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12389--12389
 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12394--12394
 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12400--12400
 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
Overfull \hbox (3.70428pt too wide) in paragraph at lines 12401--12401
 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[3026]
Underfull \hbox (badness 10000) in paragraph at lines 12470--12472
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 12470--12472
\T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or
[3027] [3028]
Underfull \hbox (badness 10000) in paragraph at lines 12600--12601
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3029] [3030]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12681--12681
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12682--12682
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 
[3031] [3032]
Underfull \hbox (badness 10000) in paragraph at lines 12833--12834
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3033] [3034] [3035] [3036] [3037]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13083--13083
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[3038]
Underfull \hbox (badness 10000) in paragraph at lines 13144--13146
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3039] [3040]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13306
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 13303--13306
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 13303--13306
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[3041] [3042]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13387--13387
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[3043]
Underfull \hbox (badness 10000) in paragraph at lines 13432--13438
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 13432--13438
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[3044] [3045] [3046]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 13646--13646
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 
Underfull \vbox (badness 10000) has occurred while \output is active [3047]
Underfull \vbox (badness 10000) has occurred while \output is active [3048]
Underfull \hbox (badness 10000) in paragraph at lines 13749--13757
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 13775--13776
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 3396) in paragraph at lines 14035--14038
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14080--14082
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[3054] [3055] [3056] [3057] [3058] [3059]
Underfull \hbox (badness 10000) in paragraph at lines 14361--14364
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-
Underfull \hbox (badness 3068) in paragraph at lines 14361--14364
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 14394--14398
[][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10
 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063] [3064]
Underfull \hbox (badness 2158) in paragraph at lines 14684--14684
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3065] [3066]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14763--14763
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3067] [3068]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14897--14897
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3069] [3070]
Underfull \hbox (badness 4846) in paragraph at lines 15028--15031
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[3071] [3072] [3073] [3074] [3075] [3076] [3077] [3078] [3079] [3080] [3081]
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16231--16231
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3091] [3092] [3093]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 16441--16441
 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1, 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 16443--16443
 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16445--16445
 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[] 
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 16465--16466
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 16465--16466
\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected
 by \T1/pcr/m/n/10 ar.row
[3095] [3096] [3097] [3098]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16653--16653
 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16654--16654
 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16666--16666
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3099] [3100] [3101]) (./nlme-pkg.tex [3102]
Chapter 25.
[3103]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3104]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3105] [3106] [3107] [3108] [3109]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3110] [3111]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611
 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621
 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[] 
[3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[3120]
Underfull \hbox (badness 5446) in paragraph at lines 1147--1149
[]\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h
tm\T1/ptm/m/n/10 ', the first edi-tion of
[3121] [3122] [3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 10000) in paragraph at lines 1630--1633
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[3128]
Underfull \hbox (badness 3780) in paragraph at lines 1647--1649
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[3129] [3130] [3131] [3132] [3133]
Underfull \hbox (badness 2042) in paragraph at lines 1996--2002
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3134]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3135]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3136] [3137]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[3138]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3139] [3140] [3141] [3142] [3143] [3144] [3145] [3146]
Underfull \hbox (badness 10000) in paragraph at lines 2849--2853
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[3147] [3148] [3149] [3150] [3151] [3152pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d
uplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box 
                                                  
l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE)
                                                  ] [3153] [3154] [3155]
[3156] [3157] [3158]
Underfull \hbox (badness 6493) in paragraph at lines 3585--3593
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166] [3167] [3168] [3169]
[3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180]
[3181] [3182]
Underfull \hbox (badness 10000) in paragraph at lines 5165--5169
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[3183] [3184] [3185] [3186] [3187] [3188] [3189]
Underfull \hbox (badness 10000) in paragraph at lines 5597--5600
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] [3198]
Underfull \hbox (badness 2799) in paragraph at lines 6103--6109
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[3199]
Underfull \hbox (badness 7133) in paragraph at lines 6164--6168
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3200]
Underfull \hbox (badness 2057) in paragraph at lines 6248--6259
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[3201]
Underfull \hbox (badness 10000) in paragraph at lines 6312--6314
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3202] [3203] [3204] [3205]
Underfull \hbox (badness 7133) in paragraph at lines 6562--6566
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[3206]
Underfull \hbox (badness 10000) in paragraph at lines 6661--6667
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6688--6688
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3207]
Underfull \hbox (badness 10000) in paragraph at lines 6726--6728
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3208]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6756--6756
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3209] [3210] [3211]
Underfull \hbox (badness 10000) in paragraph at lines 6999--7006
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,
[3212]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7017--7017
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7022--7022
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7044--7046
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[3213] [3214] [3215]
Underfull \hbox (badness 10000) in paragraph at lines 7259--7264
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[3216] [3217] [3218]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7419
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-
Underfull \hbox (badness 10000) in paragraph at lines 7411--7419
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to
Underfull \hbox (badness 4036) in paragraph at lines 7411--7419
\T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2
0 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7434--7437
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[3219] [3220] [3221]
Underfull \hbox (badness 3354) in paragraph at lines 7650--7652
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 8162--8179
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8162--8179
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8205--8205
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8214--8236
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3230] [3231] [3232] [3233] [3234]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8479--8479
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8527--8529
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3235]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8578 \aliasA{sigma}{lmeObject}{sigma}
                                        [3236] [3237] [3238] [3239] [3240]
[3241] [3242] [3243] [3244] [3245] [3246] [3247]
Underfull \hbox (badness 10000) in paragraph at lines 9330--9337
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9341--9341
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3248]
Underfull \hbox (badness 6300) in paragraph at lines 9423--9426
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[3249] [3250] [3251] [3252]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3253]
Underfull \hbox (badness 10000) in paragraph at lines 9712--9715
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9756--9759
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9756--9759
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[3254] [3255] [3256] [3257] [3258] [3259] [3260] [3261]
Underfull \hbox (badness 7291) in paragraph at lines 10220--10222
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[3262] [3263] [3264]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10436--10436
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3265]
Underfull \hbox (badness 1596) in paragraph at lines 10465--10491
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3266] [3267] [3268]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10641--10641
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3269] [3270]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10792--10792
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10803--10808
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb
[][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p
cr/m/n/10 nlm[][][]
[3271]
Underfull \hbox (badness 8075) in paragraph at lines 10825--10829
[]\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m
/n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control=
Underfull \hbox (badness 10000) in paragraph at lines 10844--10846
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10880--10880
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3272] [3273] [3274] [3275]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11136--11136
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11137--11137
 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0;  ("matrix" in older R)[] 
[3276] [3277] [3278] [3279] [3280] [3281]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11527--11527
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3282] [3283] [3284] [3285] [3286] [3287]
Underfull \hbox (badness 6268) in paragraph at lines 11914--11924
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[3288] [3289] [3290] [3291]
Underfull \hbox (badness 10000) in paragraph at lines 12175--12181
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 6876) in paragraph at lines 12497--12499
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i
ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object
 \T1/ptm/m/n/10 will be con-structed from
[3297] [3298]
Underfull \hbox (badness 2452) in paragraph at lines 12653--12660
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3299]
Underfull \hbox (badness 10000) in paragraph at lines 12718--12724
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[3300] [3301] [3302] [3303] [3304] [3305] [3306] [3307] [3308]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13307--13307
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3309] [3310] [3311] [3312] [3313]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13672--13672
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3314]
Underfull \hbox (badness 10000) in paragraph at lines 13699--13702
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
[3315]
Underfull \hbox (badness 1838) in paragraph at lines 13742--13749
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13742--13749
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13799--13799
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3316]
Underfull \hbox (badness 10000) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13806--13809
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
Underfull \hbox (badness 4582) in paragraph at lines 13834--13837
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 10000) in paragraph at lines 13834--13837
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l
abels") \T1/ptm/m/n/10 and
[3317]
Underfull \hbox (badness 10000) in paragraph at lines 13914--13917
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a
[3318]
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\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3319]
Underfull \hbox (badness 10000) in paragraph at lines 14008--14010
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3320] [3321] [3322] [3323]
Underfull \hbox (badness 1215) in paragraph at lines 14288--14290
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3324] [3325] [3326] [3327]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14532--14532
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3328] [3329] [3330] [3331] [3332] [3333] [3334] [3335] [3336]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15185 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15185 ...Extract Random Effects}{random.effects}
                                                   [3337] [3338] [3339]
[3340] [3341] [3342] [3343] [3344] [3345] [3346]
Underfull \hbox (badness 2126) in paragraph at lines 15825--15829
[]\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199
7). Phar-ma-coki-net-
[3347]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15833--15833
 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15852--15852
 []    \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718
4, tol = 1.5e-5),[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 15853--15853
 []              \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex),              
   tol = 7e-7)[] 
[3348]
Underfull \hbox (badness 1009) in paragraph at lines 15883--15892
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3349] [3350]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 16030--16030
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3351] [3352] [3353] [3354] [3355]
Underfull \hbox (badness 10000) in paragraph at lines 16365--16371
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3356]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16396--16396
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3357] [3358] [3359] [3360] [3361] [3362] [3363]
Underfull \hbox (badness 1728) in paragraph at lines 16885--16888
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3364] [3365] [3366] [3367] [3368]
Underfull \hbox (badness 1867) in paragraph at lines 17220--17229
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for
Underfull \hbox (badness 5563) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" 
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener
al
Underfull \hbox (badness 10000) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for
Underfull \hbox (badness 7397) in paragraph at lines 17220--17229
\T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin
ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and
[3369]
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[]\T1/pcr/m/n/10 "Constant plus power of variance
Underfull \hbox (badness 10000) in paragraph at lines 17292--17293
[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3370] [3371] [3372] [3373]
Underfull \hbox (badness 10000) in paragraph at lines 17542--17550
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstProp[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varFixed[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]\T1/ptm/m/n/10 ,
[3374] [3375] [3376] [3377]
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 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use 
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 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[] 
[3378] [3379] [3380] [3381] [3382] [3383]
Underfull \hbox (badness 10000) in paragraph at lines 18252--18262
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18252--18262
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3384]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3385]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3386]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3387]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3388]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
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[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18576--18585
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,
[3389]
Underfull \hbox (badness 3579) in paragraph at lines 18615--18620
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3390] [3391]
Underfull \hbox (badness 1009) in paragraph at lines 18761--18770
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3392] [3393]
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\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3394] [3395] [3396] [3397] [3398] [3399] [3400] [3401] [3402]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.multinom.1}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3403]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3404] [3405] [3406]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3407]
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 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 
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 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3408] [3409]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3410]) (./rpart-pkg.tex
Chapter 27.
[3411] [3412] [3413] [3414]
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 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3415] [3416] [3417] [3418]
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[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3419] [3420]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3421] [3422]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3423]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3424] [3425] [3426]
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 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 
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 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3427]
Underfull \hbox (badness 2846) in paragraph at lines 1228--1230
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3428]
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 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 
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 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3429] [3430] [3431] [3432] [3433] [3434]
Underfull \hbox (badness 1565) in paragraph at lines 1745--1748
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3435] [3436]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3437] [3438] [3439]) (./spatial-pkg.tex [3440]
Chapter 28.
[3441] [3442] [3443] [3444] [3445] [3446]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3447] [3448] [3449] [3450] [3451] [3452] [3453] [3454] [3455] [3456] [3457]
[3458] [3459]) (./survival-pkg.tex [3460]
Chapter 29.
[3461] [3462]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
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 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
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 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3463] [3464]
Underfull \hbox (badness 6412) in paragraph at lines 282--284
[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as 
long as
[3465] [3466]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.382 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.382 ... Myelogenous Leukemia survival data}{aml}
                                                   [3467]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 
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 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3468]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3469] [3470]
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[3471] [3472]
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 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival 
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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3473] [3474]
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 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3475] [3476] [3477]
Underfull \hbox (badness 1097) in paragraph at lines 1106--1108
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3478] [3479]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3480]
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 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter, 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1308 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3481]
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[]\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea
led by
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 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
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 []  \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[] 
[3482] [3483] [3484]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1575--1575
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
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 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE) 
[3485] [3486] [3487] [3488] [3489]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend \T1/pcr/m/n/10 survival:: \T1/pt
m/m/n/10 onto ev-er-thing, in-clud-ing the spe-
Underfull \hbox (badness 10000) in paragraph at lines 1938--1953
\T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t
ime,status) ~ age +
[3490]
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[][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp
h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 pspline[][][]\T1/ptm/m/n/10 ,
[3491]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2649--2649
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
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 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3500] [3501] [3502]
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 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3503] [3504] [3505]
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[3506] [3507]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3249--3249
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3508]
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 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 
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[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
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 []        \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[] 
[3509] [3510]
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 []                 \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3511] [3512]
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 [] [] 
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[3514]
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 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3515] [3516] [3517] [3518] [3519] [3520] [3521]
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 []                    \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] 
[3522] [3523]
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 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[] 
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 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] 
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 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1])  # differences: yhat[2:
4] - yhat[1][] 
[3524]
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[3526] [3527] [3528] [3529] [3530]
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 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3531] [3532] [3533]
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 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3534]
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 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3535]
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 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3536]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3537]
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 []  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[] 
[3538]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3539] [3540]
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 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1
=FALSE, ...) 
[3541] [3542]
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 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
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 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3543] [3544]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3545]
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3546]
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 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
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 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3547] [3548] [3549] [3550] [3551] [3552]
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 []       \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[] 
[3553] [3554] [3555]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
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\T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and
[3556] [3557] [3558] [3559] [3560]
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 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[] 
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 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[] 
[3561] [3562]
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 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE) 
[3563]
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 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)]  # rem
ove duplicates[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7008 ...ata from a soldering experiment}{solder}
                                                   [3564] [3565]
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 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3566] [3567] [3568] [3569] [3570]
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 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
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 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3571] [3572] [3573] [3574]
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 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3575] [3576] [3577] [3578]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant
ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st
ruct a sur-vival curve us-ing
[3579] [3580]
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 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)", 
[3581]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3582] [3583]
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 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3584]
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3585]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3586] [3587] [3588] [3589]
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[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8876--8876
 []        \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
 ctype,[] 
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3590] [3591] [3592]
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 []        \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[] 
[3593]
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[]\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt
m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de-
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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-
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\T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming-
harrington" which is equiv-
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\T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh
2" which is equiv-a-lent to
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[3595]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3596] [3597] [3598] [3599] [3600]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3601]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # 
use concordance 
[3602] [3603] [3604]
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\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 9986--9993
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3605]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3606] [3607] [3608]
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 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3609]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
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 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3610] [3611] [3612] [3613] [3614]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 
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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3615] [3616] [3617] [3618] [3619] [3620] [3621]
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 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3622] [3623] [3624]) (./fullrefman.ind [3625] [3626] [3627] [3628] [3629]
[3630] [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640]
[3641] [3642] [3643] [3644] [3645] [3646] [3647] [3648]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
[3649]
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3650] [3651] [3652] [3653] [3654] [3655]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3656]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3657] [3658] [3659] [3660] [3661] [3662] [3663] [3664] [3665]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method 
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[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method 
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[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,ANY-method 
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[]\T1/pcr/m/n/10 [,Matrix,missing,index,missing-method 
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[]\T1/pcr/m/n/10 [,Matrix,missing,missing,logical-method 
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[3666]
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[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method 
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}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again.
[1] Chapter 2 [2] [3] [4] [5] [6]
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 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, 
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@textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https://  doi.  org/ 
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[7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17]
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@texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia
l-ized ver-sions of
Chapter 4 [18] Chapter 5 [19] [20] [21] [22] [23] Chapter 6 [24] [25]
Chapter 7 [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37]
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[41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] )
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(/builddir/build/BUILD/R-4.1.0/doc/manual/R-FAQ.toc) Chapter 1
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[7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17]
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Chapter 4 [18] Chapter 5 [19] [20] [21] [22] [23] Chapter 6 [24] [25]
Chapter 7 [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37]
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[38]
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[41] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] )
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}] [2] [-1] Chapter 1
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[]@textrm The tar-balls are avail-able from [][]@texttt https://  stat.  ethz. 
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[1] Chapter 2 [2] Cross reference values unknown; you must run TeX again.
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[26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34]
[35] Appendix A [36] [37] [38]
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[39] [40] [41] [42] [43] [44] [45] [46] [47] [48] Appendix B [49] [50] [51]
[52] [53] Appendix C [54] [55] [56] [57] [58]
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[70] [71] (Function and variable index) [72]
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(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.p
fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
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dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmtt9.pfb>
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(/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
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(/builddir/build/BUILD/R-4.1.0/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
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}] [2] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.toc [-1] [-2])
[-3] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.toc)
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[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]
Chapter 3 [15] [16]
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[26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34]
[35] Appendix A [36] [37] [38]
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[39] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51]
[52] [53] Appendix C [54] [55] [56] [57] [58]
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[70] [71] (Function and variable index) [72]
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(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt9.pfb>
Output written on R-admin.pdf (80 pages, 522310 bytes).
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[-3] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.toc)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.toc) Chapter 1
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[]@textrm The tar-balls are avail-able from [][]@texttt https://  stat.  ethz. 
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[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]
Chapter 3 [15] [16]
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Chapter 4 [17] [18] [19] Chapter 5 [20] Chapter 6 [21] [22] [23]
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[26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34]
[35] Appendix A [36] [37] [38]
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[39] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51]
[52] [53] Appendix C [54] [55] [56] [57] [58]
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[70] [71] (Function and variable index) [72]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.vrs) (Concept index) [73]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-admin.cps)
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Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14]
[15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23]
[24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
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(/builddir/build/BUILD/R-4.1.0/doc/manual/R-data.toc) (Acknowledgements)
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Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14]
[15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23]
[24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
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(/builddir/build/BUILD/R-4.1.0/doc/manual/R-data.toc) (Acknowledgements)
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[]@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore
ign @textrm (@texttt https://  CRAN.  R-project.  org/
Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14]
[15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23]
[24] Chapter 8 [25] Chapter 9 [26] Appendix A [27]
(Function and variable index) [28]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-data.vrs [29]) (Concept index)
[30] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-data.cps) [31] )
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}] [2] [-1] (Acknowledgements) Chapter 1 [1]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
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, quiet = TRUE)[] 
[18] [19] [20] [21] [22] [23] [24] [25]
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[][][][][]@smalltt https://  www.  openmp.  org/  [][][]@smallrm , [][]@smalltt
 https://  en.  wikipedia.  org/  wiki/  OpenMP[][][]@smallrm , [][]@smalltt ht
tps://  hpc.  llnl.  gov/
[26] [27] [28]
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pp model/*/*.cpp model/*/*/*.cpp)[] 
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a07models.o $(SOURCES:.cpp=.o)[] 
[29] [30] [31]
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11PICFLAGS)")[] 
[32]
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[][][]@smallrm See [][]@smalltt https://  isocpp.  org/  std/  standing-documen
ts/  sd-6-sg10-feature-test-recommendations[][][] @smallrm or
[33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
[48] [49] [50]
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PICFLAGS`[] 
[51] [52] [53] [54] [55]
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ersion")[] 
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= "."))[] 
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vailable")[] 
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version 52.0[] 
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[57] [58] [59] [60]
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  gnu.  org/  onlinedocs/  gcc/
[61] [62] [63]
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[64]
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[][][]@smallrm See [][]@smalltt https://  prereleases.  llvm.  org/  11.  0.  0
/  rc2/  tools/  clang/  docs/  ReleaseNotes.  html#
[65] [66] [67] [68] [69]
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[]@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https://  R-Forge.  r-pro
ject.  org[]@textrm )[][]) and RForge
Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
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lename@texttt }[] @textrm and
[82] [83]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95]
Chapter 4 [96] [97] [98] [99] [100]
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 e.g.
[101] [102] [103]
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l#  controlling-code-generation[][][]@textrm ,
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[][][]@smallrm see [][]@smalltt https://  llvm.  org/  devmtg/  2014-04/  PDFs/
  LightningTalks/  EuroLLVM%202014%20--%20container%20overflow.
[104]
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[105]
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[106]
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[107] [108] [109] [110] [111]
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runk/  CRAN/  QA/  Simon/  R-build/  fixpathR[][][]@smallrm :
[112]
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ation [-Wlto-type-mismatch][] 
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 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to 
INTEGER(4)[] 
Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[123] [124] [125] [126] [127] [128] [129]
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" -lpackB[] 
[130] [131] [132] [133] [134] [135] [136] [137] [138]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150]
[151]
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[153] Chapter 6 [154] [155] [156] [157] [158] [159] [160]
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[]@textrm Passing a variable-length string from C to For-tran is trick-ier, but
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[][]@texttt https://  software.  intel.  com/  content/  www/  us/  en/  develo
p/  documentation/
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@texttt fortran-compiler-oneapi-dev-guide-and-reference/  top/  compiler-refere
nce/
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@texttt mixed-language-programming/  standard-tools-for-interoperability/  bind
.  html[][][]
[161] [162] [163] [164] [165] [166] [167] [168] [169]
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[175]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [176] [177] Chapter 8 [178] [179] [180]
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tatic libR[] 
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[182] [183] [184] [185] [186] [187]
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[188]
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}] [2] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.toc [-1] [-2] [-3])
[-4] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.toc)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.toc) (Acknowledgements)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.aux) Chapter 1 [1]
Writing index file R-exts.cp
[2] [3] [4] [5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
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, "--no-test-load")[] 
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 []        @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL
, quiet = TRUE)[] 
[18] [19] [20] [21] [22] [23] [24] [25]
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[][][][][]@smalltt https://  www.  openmp.  org/  [][][]@smallrm , [][]@smalltt
 https://  en.  wikipedia.  org/  wiki/  OpenMP[][][]@smallrm , [][]@smalltt ht
tps://  hpc.  llnl.  gov/
[26] [27] [28]
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pp model/*/*.cpp model/*/*/*.cpp)[] 
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a07models.o $(SOURCES:.cpp=.o)[] 
[29] [30] [31]
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[32]
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[][][]@smallrm See [][]@smalltt https://  isocpp.  org/  std/  standing-documen
ts/  sd-6-sg10-feature-test-recommendations[][][] @smallrm or
[33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
[48] [49] [50]
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ILITY)" \[] 
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PICFLAGS`[] 
[51] [52] [53] [54] [55]
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ersion")[] 
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= "."))[] 
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vailable")[] 
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version 52.0[] 
[56]
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e looked for
[57] [58] [59] [60]
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  gnu.  org/  onlinedocs/  gcc/
[61] [62] [63]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[64]
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[][][]@smallrm See [][]@smalltt https://  prereleases.  llvm.  org/  11.  0.  0
/  rc2/  tools/  clang/  docs/  ReleaseNotes.  html#
[65] [66] [67] [68] [69]
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[]@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https://  R-Forge.  r-pro
ject.  org[]@textrm )[][]) and RForge
Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[82] [83]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95]
Chapter 4 [96] [97] [98] [99] [100]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[101] [102] [103]
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@textrm See [][]@texttt https://  clang.  llvm.  org/  docs/  UsersManual.  htm
l#  controlling-code-generation[][][]@textrm ,
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[][][]@smallrm see [][]@smalltt https://  llvm.  org/  devmtg/  2014-04/  PDFs/
  LightningTalks/  EuroLLVM%202014%20--%20container%20overflow.
[104]
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[105]
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[106]
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[107] [108] [109] [110] [111]
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[][][]@smallrm See [][]@smalltt https://  svn.  r-project.  org/  R-dev-web/  t
runk/  CRAN/  QA/  Simon/  R-build/  fixpathR[][][]@smallrm :
[112]
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ration [-Wlto-type-mismatch][] 
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ation [-Wlto-type-mismatch][] 
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 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to 
INTEGER(4)[] 
Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[123] [124] [125] [126] [127] [128]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[129] [130] [131] [132] [133] [134] [135] [136] [137] [138]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150]
[151]
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NilValue);[] 
[152]
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 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE
_ANY} cetype_t;[] 
[153] Chapter 6 [154] [155] [156] [157] [158] [159] [160]
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[]@textrm Passing a variable-length string from C to For-tran is trick-ier, but
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[][]@texttt https://  software.  intel.  com/  content/  www/  us/  en/  develo
p/  documentation/
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@texttt fortran-compiler-oneapi-dev-guide-and-reference/  top/  compiler-refere
nce/
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@texttt mixed-language-programming/  standard-tools-for-interoperability/  bind
.  html[][][]
[161] [162] [163] [164] [165] [166] [167] [168] [169]
Warning: unbalanced parentheses in @def... [170] [171] [172] [173] [174]
[175]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [176] [177] Chapter 8 [178] [179] [180]
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tatic libR[] 
[181]
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nst char *);[] 
[182] [183] [184] [185] [186] [187]
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tive in-stall and
[188]
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 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
[189] (Function and variable index) [190]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.vrs [191] [192] [193])
(Concept index) [194] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.cps
[195]) [196] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></
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e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pf
b>
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}] [2] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.toc [-1] [-2] [-3])
[-4] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.toc)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.toc) (Acknowledgements)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-exts.aux) Chapter 1 [1]
Writing index file R-exts.cp
[2] [3] [4] [5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
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, "--no-test-load")[] 
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 []        @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL
, quiet = TRUE)[] 
[18] [19] [20] [21] [22] [23] [24] [25]
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[][][][][]@smalltt https://  www.  openmp.  org/  [][][]@smallrm , [][]@smalltt
 https://  en.  wikipedia.  org/  wiki/  OpenMP[][][]@smallrm , [][]@smalltt ht
tps://  hpc.  llnl.  gov/
[26] [27] [28]
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pp model/*/*.cpp model/*/*/*.cpp)[] 
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a07models.o $(SOURCES:.cpp=.o)[] 
[29] [30] [31]
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[][][]@smallrm Some changes are linked from [][]@smalltt https://  isocpp.  org
/  std/  standing-documents/
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[32]
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[][][]@smallrm See [][]@smalltt https://  isocpp.  org/  std/  standing-documen
ts/  sd-6-sg10-feature-test-recommendations[][][] @smallrm or
[33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
[48] [49] [50]
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PICFLAGS`[] 
[51] [52] [53] [54] [55]
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ersion")[] 
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= "."))[] 
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vailable")[] 
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version 52.0[] 
[56]
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[61] [62] [63]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[64]
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[][][]@smallrm See [][]@smalltt https://  prereleases.  llvm.  org/  11.  0.  0
/  rc2/  tools/  clang/  docs/  ReleaseNotes.  html#
[65] [66] [67] [68] [69]
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[]@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https://  R-Forge.  r-pro
ject.  org[]@textrm )[][]) and RForge
Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[82] [83]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95]
Chapter 4 [96] [97] [98] [99] [100]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
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[101] [102] [103]
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@textrm See [][]@texttt https://  clang.  llvm.  org/  docs/  UsersManual.  htm
l#  controlling-code-generation[][][]@textrm ,
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[][][]@smallrm see [][]@smalltt https://  llvm.  org/  devmtg/  2014-04/  PDFs/
  LightningTalks/  EuroLLVM%202014%20--%20container%20overflow.
[104]
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[105]
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[107] [108] [109] [110] [111]
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[][][]@smallrm See [][]@smalltt https://  svn.  r-project.  org/  R-dev-web/  t
runk/  CRAN/  QA/  Simon/  R-build/  fixpathR[][][]@smallrm :
[112]
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 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to 
INTEGER(4)[] 
Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]
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riv, PACKAGE = "splines")[] 
[123] [124] [125] [126] [127] [128]
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" -lpackB[] 
[129] [130] [131] [132] [133] [134] [135] [136] [137] [138]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150]
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[153] Chapter 6 [154] [155] [156] [157] [158] [159] [160]
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[]@textrm Passing a variable-length string from C to For-tran is trick-ier, but
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[][]@texttt https://  software.  intel.  com/  content/  www/  us/  en/  develo
p/  documentation/
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nce/
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.  html[][][]
[161] [162] [163] [164] [165] [166] [167] [168] [169]
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[175]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [176] [177] Chapter 8 [178] [179] [180]
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[182] [183] [184] [185] [186] [187]
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[188]
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 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
[189] (Function and variable index) [190]
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Chapter 1 [1]
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al/images/QQ.pdf> [35] [36] </builddir/build/BUILD/R-4.1.0/doc/manual/images/ic
e.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45]
[46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58]
[59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] </buildd
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[77] Chapter 14 [78] [79]
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93]
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}] [2] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.toc [-1] [-2] [-3])
[-4] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.toc)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.toc) (Preface)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.aux) Chapter 1 [1]
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[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13]
[14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24]
Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] </bu
ilddir/build/BUILD/R-4.1.0/doc/manual/images/hist.pdf> [34] </builddir/build/BU
ILD/R-4.1.0/doc/manual/images/ecdf.pdf> </builddir/build/BUILD/R-4.1.0/doc/manu
al/images/QQ.pdf> [35] [36] </builddir/build/BUILD/R-4.1.0/doc/manual/images/ic
e.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45]
[46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58]
[59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] </buildd
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[77] Chapter 14 [78] [79]
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93]
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[98] [99] )
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(/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.toc) (Preface)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.aux) Chapter 1 [1]
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[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13]
[14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24]
Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] </bu
ilddir/build/BUILD/R-4.1.0/doc/manual/images/hist.pdf> [34] </builddir/build/BU
ILD/R-4.1.0/doc/manual/images/ecdf.pdf> </builddir/build/BUILD/R-4.1.0/doc/manu
al/images/QQ.pdf> [35] [36] </builddir/build/BUILD/R-4.1.0/doc/manual/images/ic
e.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45]
[46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58]
[59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] </buildd
ir/build/BUILD/R-4.1.0/doc/manual/images/fig11.pdf> [71] </builddir/build/BUILD
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[77] Chapter 14 [78] [79]
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93]
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[96] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-intro.cps [97]) Appendix F
[98] [99] )
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
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@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
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[44] Chapter 8 [45]
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hoice of
[47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10
[58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index)
[62]
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
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@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45]
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s://  CRAN.  R-project.  org/
[46]
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 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10
[58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index)
[62] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-ints.vrs [63])
(Concept index) [64] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-ints.cps)
[65] )
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[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15]
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 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 
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ics with methods[] 
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(group)generic[] 
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" "ANY#ldiMatrix" "ANY#Matrix"[] 
[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
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@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45]
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s://  CRAN.  R-project.  org/
[46]
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 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10
[58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index)
[62] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-ints.vrs [63])
(Concept index) [64] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-ints.cps)
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[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
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[46] [47] [48] [49] [50] (Function and Variable Index) [51]
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[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.vrs [52]) (Concept Index)
[53] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.cps) Appendix A [54]
[55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
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Output written on R-lang.pdf (60 pages, 375640 bytes).
Transcript written on R-lang.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdfetex)
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}] [2] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.toc [-1] [-2]) [-3]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.toc)
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.toc) Chapter 1
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.aux)
Writing index file R-lang.cp
Chapter 2 [1] [2]
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 @textbf storage.mode| 
[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
Underfull \hbox (badness 10000) in paragraph at lines 4353--4355
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51]
(/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.vrs [52]) (Concept Index)
[53] (/builddir/build/BUILD/R-4.1.0/doc/manual/R-lang.cps) Appendix A [54]
[55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf
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Output written on R-lang.pdf (60 pages, 375631 bytes).
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+ rm -rf /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64
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+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64
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gcc -m64 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -DR_HOME='"/usr/lib64/R"' \
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+ rm -f /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/info/dir.old
+ mkdir -p /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/R
+ install -p CAPABILITIES /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/R
+ cd src/nmath/standalone
+ make install DESTDIR=/builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/src/include'
make[1]: 'Rmath.h' is up to date.
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/src/include'
+ mkdir -p /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/etc/ld.so.conf.d
+ echo /usr/lib64/R/lib
+ mkdir -p /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/R/library
+ touch -r README /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/R/CAPABILITIES
+ touch -r README doc/manual/R-FAQ.pdf doc/manual/R-admin.pdf doc/manual/R-data.pdf doc/manual/R-exts.pdf doc/manual/R-intro.pdf doc/manual/R-ints.pdf doc/manual/R-lang.pdf doc/manual/fullrefman.pdf
+ touch -r README /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/bin/R
+ sed -i 's|\..\/\..|/usr/lib64/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/R/html/packages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/bkde.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/bkde2D.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/bkfe.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/dpih.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/dpik.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/dpill.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/html/locpoly.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Aids2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Animals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Boston.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Cars93.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Cushings.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/DDT.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/GAGurine.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Insurance.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/MASS-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Melanoma.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Null.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/OME.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Pima.tr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Rabbit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Rubber.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/SP500.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Sitka.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Sitka89.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Skye.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/Traffic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/UScereal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/UScrime.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/VA.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/abbey.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/accdeaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/addterm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/anorexia.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/anova.negbin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/area.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/bacteria.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/bandwidth.nrd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/bcv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/beav1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/beav2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/biopsy.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/birthwt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/boxcox.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/cabbages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/caith.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/cats.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/cement.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/chem.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/con2tr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/confint.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/contr.sdif.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/coop.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/corresp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/cov.rob.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/cov.trob.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/cpus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/crabs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/deaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/denumerate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/dose.p.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/drivers.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/dropterm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/eagles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/epil.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/eqscplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/farms.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/fgl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/fitdistr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/forbes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/fractions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/galaxies.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/gamma.dispersion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/gamma.shape.glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/gehan.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/genotype.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/geyser.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/gilgais.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/ginv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/glm.convert.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/glm.nb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/glmmPQL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/hills.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/hist.scott.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/housing.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/huber.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/hubers.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/immer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/isoMDS.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/kde2d.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/lda.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/ldahist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/leuk.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/lm.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/lm.ridge.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/loglm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/loglm1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/logtrans.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/lqs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/mammals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/mca.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/mcycle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/menarche.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/michelson.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/minn38.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/motors.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/muscle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/mvrnorm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/negative.binomial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/newcomb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/nlschools.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/npk.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/npr1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/oats.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/painters.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/pairs.lda.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/parcoord.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/petrol.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/phones.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/plot.lda.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/plot.mca.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/plot.profile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/polr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/predict.glmmPQL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/predict.lda.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/predict.lqs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/predict.mca.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/predict.qda.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/profile.glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/qda.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/quine.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/rational.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/renumerate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/rlm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/rms.curv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/rnegbin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/road.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/rotifer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/sammon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/ships.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/shoes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/shrimp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/shuttle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/snails.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/stdres.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/steam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/html/stepAIC.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Extract.data.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Extract.factor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Extract.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Extremes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Foreign-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Foreign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Hyperbolic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ISOdatetime.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/InternalMethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/La_library.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/La_version.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Last.value.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Log.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Logic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/LongVectors.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/MathFun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Memory-limits.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Memory.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/NA.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/NULL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/NumericConstants.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Ops.Date.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Paren.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Platform.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Primitive.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Quotes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Random-user.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Random.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/RdUtils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Recall.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Reserved.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Rhome.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Round.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/S3method.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Signals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Special.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Startup.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Syntax.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.getenv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.getpid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.glob.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.info.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.localeconv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.readlink.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.setFileTime.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.setenv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.sleep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.time.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Sys.which.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Trig.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/UTF8filepaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/UseMethod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Vectorize.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/Version.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/abbreviate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/agrep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/all.equal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/all.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/allnames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/any.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/aperm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/append.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/apply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/args.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/array.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/as.Date.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/as.POSIXlt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/as.data.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/as.environment.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/as.function.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/asplit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/assign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/assignOps.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/attach.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/attr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/attributes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/autoload.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/backsolve.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/base-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/base-deprecated.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/base-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/base-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/basename.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/bincode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/bindenv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/bitwise.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/body.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/bquote.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/browser.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/browserText.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/builtins.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/by.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/c.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/call.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/callCC.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/capabilities.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/cat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/cbind.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/char.expand.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/character.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/charmatch.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/chartr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/chkDots.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/chol.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/chol2inv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/col.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/colSums.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/colnames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/commandArgs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/comment.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/complex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/conditions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/conflicts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/connections.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/contributors.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/copyright.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/crossprod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/cumsum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/curlGetHeaders.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/cut.POSIXt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/cut.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/data.class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/data.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/data.matrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dataframeHelpers.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/date.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dcf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/debug.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/delayedAssign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/deparse.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/deparseOpts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/det.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/detach.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dev.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/diag.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/diff.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/difftime.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dimnames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/do.call.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dontCheck.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dots.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/double.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dput.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/drop.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/droplevels.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dump.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/duplicated.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/dynload.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/eapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/eigen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/encodeString.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/environment.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/eval.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/exists.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/expand.grid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/expression.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/extSoftVersion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/factor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/file.access.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/file.choose.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/file.info.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/file.path.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/file.show.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/files.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/files2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/find.package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/findInterval.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/force.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/forceAndCall.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/formals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/format.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/format.info.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/format.pval.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/formatDL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/formatc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/function.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/funprog.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/gc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/gc.time.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/gctorture.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/get.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/getCallingDLL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/getDLLRegisteredRoutines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/getLoadedDLLs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/getNativeSymbolInfo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/gettext.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/getwd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/gl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/grep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/grepRaw.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/groupGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/grouping.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/gzcon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/hexmode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/iconv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/icuSetCollate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/identical.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/identity.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ifelse.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/integer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/interaction.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/interactive.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/invisible.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.finite.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.function.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.language.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.recursive.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.single.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/is.unsorted.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/isR.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/isS4.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/isSymmetric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/jitter.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/kappa.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/kronecker.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/l10n_info.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/labels.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/lapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/lazyload.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/length.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/lengths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/levels.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/libPaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/libcurlVersion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/library.dynam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/library.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/license.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/list.files.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/list.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/list2DF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/list2env.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/load.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/locales.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/logical.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/lower.tri.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/make.names.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/make.unique.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/mapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/marginSums.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/mat.or.vec.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/match.arg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/match.call.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/match.fun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/match.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/matmult.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/matrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/maxCol.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/mean.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/memCompress.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/memlimits.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/memory.profile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/merge.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/message.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/missing.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/mode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/name.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/names.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/nargs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/nchar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/nlevels.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/noquote.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/norm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/normalizePath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/notyet.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/nrow.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ns-dblcolon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ns-hooks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ns-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ns-load.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ns-reflect.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/ns-topenv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/numeric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/numeric_version.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/octmode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/on.exit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/order.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/outer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/parse.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/paste.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/path.expand.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/pcre_config.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/pipeOp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/plot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/pmatch.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/polyroot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/pos.to.env.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/pretty.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/print.dataframe.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/print.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/print.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/prmatrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/proc.time.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/prod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/proportions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/pushBack.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/qr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/qraux.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/quit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/range.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rank.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/raw.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rawConnection.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rawConversion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/readBin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/readChar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/readLines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/readRDS.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/readRenviron.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/readline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/reg.finalizer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/regex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/regmatches.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/replace.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rev.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/round.POSIXt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/row.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/row.names.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/rowsum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sQuote.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sample.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/save.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/scale.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/scan.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/search.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/seek.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/seq.Date.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/seq.POSIXt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/seq.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sequence.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/serialize.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/setTimeLimit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sets.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/shQuote.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/showConnections.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sink.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/slice.index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/slotOp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/socketSelect.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/solve.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sort.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/source.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/split.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sprintf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/srcfile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/standardGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/startsWith.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/stop.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/stopifnot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/strptime.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/strrep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/strsplit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/strtoi.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/strtrim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/structure.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/strwrap.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/subset.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/substitute.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/substr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/summary.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/svd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sweep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/switch.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sys.parent.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/sys.source.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/system.file.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/system.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/system.time.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/system2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/t.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/table.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/tabulate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/tapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/taskCallback.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/taskCallbackManager.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/taskCallbackNames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/tempfile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/textconnections.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/tilde.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/timezones.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/toString.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/trace.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/traceback.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/tracemem.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/transform.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/trimws.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/try.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/typeof.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/unique.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/unlink.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/unlist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/unname.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/userhooks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/utf8Conversion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/validUTF8.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/vector.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/warning.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/warnings.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/weekday.POSIXt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/which.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/which.min.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/with.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/withVisible.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/write.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/writeLines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/xtfrm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/zMachine.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/zScript.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/zapsmall.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/zpackages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/base/html/zutils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/EEF.profile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/Imp.Estimates.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/abc.ci.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/acme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/aids.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/aircondit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/amis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/aml.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/beaver.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/bigcity.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/boot-practicals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/boot.array.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/boot.ci.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/boot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/brambles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/breslow.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/calcium.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cane.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/capability.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/catsM.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cav.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cd4.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cd4.nested.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/censboot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/channing.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/claridge.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cloth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/co.transfer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/coal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/corr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cum3.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/cv.glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/darwin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/dogs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/downs.bc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/ducks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/empinf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/envelope.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/exp.tilt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/fir.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/freq.array.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/frets.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/glm.diag.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/glm.diag.plots.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/gravity.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/hirose.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/imp.weights.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/inv.logit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/islay.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/jack.after.boot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/k3.linear.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/linear.approx.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/lines.saddle.distn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/logit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/manaus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/melanoma.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/motor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/neuro.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/nitrofen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/nodal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/norm.ci.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/nuclear.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/paulsen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/plot.boot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/poisons.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/polar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/print.boot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/print.bootci.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/print.saddle.distn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/print.simplex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/remission.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/saddle.distn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/saddle.distn.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/saddle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/salinity.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/simplex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/simplex.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/smooth.f.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/sunspot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/survival.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/tau.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/tilt.boot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/tsboot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/tuna.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/urine.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/var.linear.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/boot/html/wool.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/SOM.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/batchSOM.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/condense.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/knn.cv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/knn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/knn1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/lvq1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/lvq2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/lvq3.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/lvqinit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/lvqtest.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/multiedit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/olvq1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/reduce.nn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/html/somgrid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/agnes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/agnes.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/agriculture.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/animals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/bannerplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/chorSub.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/clara.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/clara.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/clusGap.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/clusplot.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/clusplot.partition.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/cluster-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/coef.hclust.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/daisy.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/diana.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/dissimilarity.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/ellipsoidhull.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/fanny.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/fanny.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/flower.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/lower.to.upper.tri.inds.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/mona.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/mona.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/pam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/pam.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/partition.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/plantTraits.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/plot.agnes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/plot.diana.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/plot.mona.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/plot.partition.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/pltree.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/pluton.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/predict.ellipsoid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.agnes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.clara.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.diana.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.dissimilarity.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.fanny.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.mona.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/print.pam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/ruspini.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/silhouette.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/sizeDiss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/summary.agnes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/summary.clara.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/summary.diana.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/summary.mona.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/summary.pam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/twins.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/volume.ellipsoid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/votes.repub.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/html/xclara.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/codetools/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/codetools/html/checkUsage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/codetools/html/codetools.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/codetools/html/findGlobals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/codetools/html/showTree.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/compiler/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/compiler/html/compile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/AirPassengers.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/BJsales.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/BOD.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/ChickWeight.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/DNase.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/EuStockMarkets.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Formaldehyde.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/HairEyeColor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Harman23.cor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Harman74.cor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Indometh.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/InsectSprays.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/JohnsonJohnson.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/LakeHuron.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/LifeCycleSavings.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Loblolly.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Nile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Orange.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/OrchardSprays.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/PlantGrowth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Puromycin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Theoph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/Titanic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/ToothGrowth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/UCBAdmissions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/UKDriverDeaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/UKLungDeaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/UKgas.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/USAccDeaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/USArrests.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/USJudgeRatings.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/USPersonalExpenditure.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/VADeaths.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/WWWusage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/WorldPhones.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/ability.cov.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/airmiles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/airquality.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/anscombe.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/attenu.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/attitude.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/austres.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/beavers.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/cars.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/chickwts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/co2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/crimtab.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/datasets-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/discoveries.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/esoph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/euro.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/eurodist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/faithful.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/freeny.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/infert.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/iris.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/islands.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/lh.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/longley.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/lynx.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/morley.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/mtcars.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/nhtemp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/nottem.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/npk.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/occupationalStatus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/precip.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/presidents.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/pressure.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/quakes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/randu.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/rivers.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/rock.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/sleep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/stackloss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/state.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/sunspot.month.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/sunspot.year.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/sunspots.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/swiss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/treering.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/trees.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/uspop.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/volcano.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/warpbreaks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/women.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/datasets/html/zCO2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/lookup.xport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.S.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.arff.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.dbf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.dta.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.epiinfo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.mtp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.octave.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.spss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.ssd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.systat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/read.xport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/write.arff.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/write.dbf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/write.dta.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/html/write.foreign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/Devices.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/Hershey.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/Japanese.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/Type1Font.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/adjustcolor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/as.graphicsAnnot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/as.raster.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/axisTicks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/boxplot.stats.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/bringToTop.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/cairo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/cairoSymbolFont.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/check.options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/chull.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/cm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/col2rgb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/colorRamp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/colors.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/contourLines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/convertColor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/densCols.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev.capabilities.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev.capture.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev.flush.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev.interactive.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev.size.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/dev2bitmap.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/devAskNewPage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/embedFonts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/extendrange.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/getGraphicsEvent.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/grDevices-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/grSoftVersion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/gray.colors.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/gray.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/hcl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/hsv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/make.rgb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/msgWindow.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/n2mfrow.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/nclass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/palette.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/palettes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/pdf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/pdf.options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/pictex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/plotmath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/png.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/postscript.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/postscriptFonts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/pretty.Date.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/ps.options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/quartz.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/quartzFonts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/recordGraphics.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/recordplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/rgb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/rgb2hsv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/savePlot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/trans3d.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/windows.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/windows.options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/windowsFonts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/x11.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/x11Fonts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/xfig.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/xy.coords.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/xyTable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/html/xyz.coords.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/abline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/arrows.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/assocplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/axTicks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/axis.POSIXct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/axis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/barplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/box.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/boxplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/boxplot.matrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/bxp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/cdplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/clip.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/contour.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/convertXY.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/coplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/curve.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/dotchart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/filled.contour.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/fourfoldplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/graphics-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/graphics-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/grid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/hist.POSIXt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/hist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/identify.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/image.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/layout.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/legend.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/lines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/locator.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/matplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/mosaicplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/mtext.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/pairs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/panel.smooth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/par.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/persp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/pie.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.dataframe.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.design.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.factor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.raster.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.table.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.window.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plot.xy.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/plothistogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/points.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/polygon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/polypath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/rasterImage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/rect.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/rug.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/screen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/segments.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/smoothScatter.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/spineplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/stars.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/stem.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/stripchart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/strwidth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/sunflowerplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/symbols.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/text.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/title.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/units.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/xspline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/html/zAxis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/Grid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/absolute.size.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/arrow.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/calcStringMetric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/current.viewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/dataViewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/depth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/deviceLoc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/drawDetails.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/editDetails.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/editViewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/explode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/gEdit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/gPath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/getNames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/gpar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.DLapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.add.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.bezier.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.cap.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.circle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.clip.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.convert.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.copy.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.curve.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.delay.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.display.list.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.draw.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.edit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.force.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.function.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.get.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.grab.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.grep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.grill.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.grob.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.layout.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.lines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.locator.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.ls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.move.to.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.newpage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.null.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.pack.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.path.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.place.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.plot.and.legend.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.points.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.polygon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.pretty.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.raster.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.record.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.rect.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.refresh.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.remove.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.reorder.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.roundrect.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.segments.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.set.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.show.layout.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.show.viewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.text.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.xaxis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.xspline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grid.yaxis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grobCoords.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grobName.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grobWidth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/grobX.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/legendGrob.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/makeContent.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/patterns.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/plotViewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/resolveRasterSize.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/showGrob.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/showViewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/stringWidth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/unit.c.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/unit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/unit.length.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/unit.pmin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/unit.rep.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/unitType.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/valid.just.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/validDetails.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/viewport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/viewports.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/vpPath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/widthDetails.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/xDetails.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/html/xsplinePoints.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/Lattice.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/Rows.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/USMortality.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/axis.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/banking.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/barchart.table.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/barley.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/cloud.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/draw.colorkey.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/draw.key.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/environmental.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/ethanol.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/histogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/interaction.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/lattice.options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/latticeParseFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/level.colors.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/levelplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/llines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/lset.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/make.groups.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/melanoma.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/oneway.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/packet.panel.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.axis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.barchart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.bwplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.cloud.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.densityplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.dotplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.functions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.histogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.levelplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.loess.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.number.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.pairs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.parallel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.qqmath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.qqmathline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.smoothScatter.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.spline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.stripplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.superpose.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.violin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/panel.xyplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/prepanel.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/prepanel.functions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/print.trellis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/qq.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/qqmath.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/rfs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/shingles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/simpleKey.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/simpleTheme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/singer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/splom.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/strip.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/tmd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/trellis.device.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/trellis.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/trellis.par.get.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/update.trellis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/utilities.3d.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/xyplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/lattice/html/xyplot.ts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/BasicClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Classes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Classes_Details.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Documentation.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/EmptyMethodsList-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/EnvironmentClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/GenericFunctions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Introduction.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/LanguageClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/LinearMethodsList-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/MethodDefinition-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/MethodSupport.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/MethodWithNext-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/MethodsList-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/MethodsList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Methods_Details.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Methods_for_Nongenerics.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/Methods_for_S3.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/NextMethod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/ObjectsWithPackage-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/RClassUtils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/RMethodUtils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/S3Part.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/S4groupGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/SClassExtension-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/StructureClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/TraceClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/as.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/callGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/canCoerce.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/cbind2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/className.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/classRepresentation-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/classesToAM.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/dotsMethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/evalSource.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/findClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/findMethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/fixPrevious.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/genericFunction-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/getClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/getMethod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/getPackageName.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/hasArg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/implicitGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/inheritedSlotNames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/initialize-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/is.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/isSealedMethod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/languageEl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/localRefClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/method.skeleton.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/methodUtilities.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/methods-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/methods-deprecated.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/methods-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/new.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/nonStructure-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/promptClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/promptMethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/refClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/removeMethod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/representation.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/selectSuperClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setAs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setClassUnion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setGroupGeneric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setIs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setLoadActions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setMethod.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setOldClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/setSClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/show.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/showMethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/signature-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/slot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/stdRefClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/substituteDirect.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/testInheritedMethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/validObject.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/html/zBasicFunsList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/Beta.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/FFdes.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/fixDependence.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/formXtViX.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/formula.gam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/fs.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/full.score.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.check.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.convergence.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.fit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.fit3.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.fit5.post.proc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.mh.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.models.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.outer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.reparam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.scale.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.selection.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.side.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam.vcomp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gam2objective.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gamObject.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gamSim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gamlss.etamu.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gamlss.gH.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gamm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gammals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gaulss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/get.var.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gevlss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/ginla.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/gumbls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/identifiability.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/in.out.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/inSide.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/influence.gam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/initial.sp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/interpret.gam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/jagam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/k.check.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/ldTweedie.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/ldetS.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/linear.functional.terms.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/logLik.gam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/ls.size.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/magic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/magic.post.proc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/html/mgcv-FAQ.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/ACF.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Alfalfa.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Assay.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/BodyWeight.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Cefamandole.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Coef.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Covariate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Covariate.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Dialyzer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Dim.corSpatial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Dim.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Dim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Dim.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Earthquake.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Extract.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Fatigue.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Gasoline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Glucose.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Glucose2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Gun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/IGF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Initialize.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Initialize.glsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Initialize.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Initialize.lmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Initialize.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Initialize.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/LDEsysMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Machines.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/MathAchSchool.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/MathAchieve.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Matrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Matrix.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Matrix.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Meat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Milk.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Muscle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Names.formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Names.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Names.pdBlocked.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Names.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Names.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Nitrendipene.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Oats.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Orthodont.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Ovary.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Oxboys.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Oxide.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/PBG.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Phenobarb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Pixel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Quinidine.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Rail.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/RatPupWeight.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Relaxin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Remifentanil.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Soybean.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Spruce.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Tetracycline1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Tetracycline2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/VarCorr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.corExp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.corGaus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.corLin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.corRatio.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.corSpatial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.corSpher.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.default.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Variogram.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Wafer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Wheat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/Wheat2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/allCoef.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/anova.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/anova.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/as.matrix.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/as.matrix.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/as.matrix.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/asOneFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/asTable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/augPred.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/balancedGrouped.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/bdf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.gnls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.modelStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/coef.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/collapse.groupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/collapse.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/compareFits.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/comparePred.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corAR1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corARMA.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corCAR1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corCompSymm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corExp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corFactor.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corFactor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corGaus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corLin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corMatrix.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corMatrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corMatrix.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corMatrix.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corNatural.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corRatio.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corSpatial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corSpher.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/corSymm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/ergoStool.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fdHess.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fitted.glsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fitted.gnlsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fitted.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fitted.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fitted.lmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fitted.nlmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fixed.effects.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/fixef.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/formula.pdBlocked.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/formula.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/formula.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getCovariate.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getCovariate.data.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getCovariate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getCovariate.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getCovariateFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getData.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getData.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getData.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.data.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroups.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getGroupsFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getResponse.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getResponseFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/getVarCov.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gls-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/glsControl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/glsObject.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/glsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gnls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gnlsControl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gnlsObject.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gnlsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/groupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/gsummary.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/intervals.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/intervals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/intervals.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/intervals.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/isBalanced.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/isInitialized.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lmList.groupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lme.groupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lme.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lmeControl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lmeObject.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/lmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logDet.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logDet.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logDet.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logDet.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.glsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.gnls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.gnlsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.lmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/logLik.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/model.matrix.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/needUpdate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/needUpdate.modelStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlme.nlsList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlmeControl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlmeObject.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlsList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/nlsList.selfStart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pairs.compareFits.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pairs.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pairs.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdBlocked.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdCompSymm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdConstruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdConstruct.pdBlocked.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdDiag.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdFactor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdFactor.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdIdent.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdLogChol.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdMatrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdMatrix.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdNatural.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pdSymm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/phenoModel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.ACF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.Variogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.augPred.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.compareFits.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.intervals.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.nffGroupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.nfnGroupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.nmGroupedData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.ranef.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/plot.ranef.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/pooledSD.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/predict.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/predict.gnls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/predict.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/predict.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/predict.nlme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/print.summary.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/print.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/qqnorm.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/qqnorm.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/quinModel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/random.effects.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/ranef.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/ranef.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/recalc.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/recalc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/recalc.modelStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/recalc.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/recalc.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.glsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.gnlsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.lmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/residuals.nlmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/simulate.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/solve.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/solve.reStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/splitFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.corStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.lmList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.lme.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.modelStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.nlsList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.pdMat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/summary.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/update.modelStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/update.varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varComb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varConstPower.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varConstProp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varExp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varFixed.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varFunc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varIdent.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varPower.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varWeights.glsStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varWeights.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/html/varWeights.lmeStruct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/class.ind.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/multinom.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/nnet.Hess.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/nnet.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/predict.nnet.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/html/which.is.max.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/RngStream.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/children.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/clusterApply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/detectCores.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/makeCluster.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/mcaffinity.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/mcfork.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/mclapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/mcparallel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/parallel-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/pvec.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/html/splitIndices.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/car.test.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/car90.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/cu.summary.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/kyphosis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/labels.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/meanvar.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/na.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/path.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/plot.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/plotcp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/post.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/predict.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/print.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/printcp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/prune.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/residuals.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/rpart-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/rpart.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/rpart.exp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/rpart.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/rsq.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/snip.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/solder.balance.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/stagec.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/summary.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/text.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/html/xpred.rpart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/Kaver.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/Kenvl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/Kfn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/Psim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/SSI.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/Strauss.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/anova.trls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/correlogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/expcov.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/ppgetregion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/ppinit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/pplik.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/ppregion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/predict.trls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/prmat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/semat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/surf.gls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/surf.ls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/trls.influence.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/trmat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/html/variogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/asVector.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/backSpline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/bs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/interpSpline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/ns.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/periodicSpline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/polySpline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/predict.bSpline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/predict.bs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/splineDesign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/splineKnots.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/splineOrder.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/splines-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/html/xyVector.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/AIC.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ARMAacf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ARMAtoMA.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Beta.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Binomial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Cauchy.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Chisquare.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Distributions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Exponential.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Fdist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/GammaDist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Geometric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/HoltWinters.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Hypergeometric.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/IQR.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/KalmanLike.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Logistic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Lognormal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Multinom.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/NLSstAsymptotic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/NLSstClosestX.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/NLSstLfAsymptote.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/NLSstRtAsymptote.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/NegBinomial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Normal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Pair.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Poisson.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSD.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSasymp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSasympOff.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSasympOrig.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSbiexp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSfol.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSfpl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSgompertz.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSlogis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSmicmen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SSweibull.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/SignRank.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/StructTS.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/TDist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Tukey.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/TukeyHSD.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Uniform.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Weibull.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/Wilcoxon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/acf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/acf2AR.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/add1.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/addmargins.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/aggregate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/alias.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/anova.glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/anova.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/anova.lm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/anova.mlm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ansari.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/aov.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/approxfun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ar.ols.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/arima.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/arima.sim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/arima0.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/as.hclust.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/asOneSidedFormula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ave.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/bandwidth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/bartlett.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/binom.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/biplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/biplot.princomp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/birthday.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/box.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cancor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/case.names.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/checkMFClasses.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/chisq.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cmdscale.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/coef.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/complete.cases.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/confint.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/constrOptim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/contrast.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/contrasts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/convolve.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cophenetic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cor.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cov.wt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cpgram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/cutree.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/decompose.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/delete.response.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/dendrapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/dendrogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/density.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/deriv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/deviance.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/df.residual.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/diffinv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/dist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/dummy.coef.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ecdf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/eff.aovlist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/effects.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/embed.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/expand.model.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/extractAIC.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/factanal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/factor.scope.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/family.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/fft.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/filter.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/fisher.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/fitted.values.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/fivenum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/fligner.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/formula.nls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/friedman.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ftable.formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ftable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/getInitial.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/glm.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/glm.summaries.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/hclust.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/heatmap.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/identify.hclust.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/influence.measures.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/integrate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/interaction.plot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/is.empty.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/isoreg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/kernapply.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/kernel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/kmeans.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/kruskal.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ks.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ksmooth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lag.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lag.plot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/line.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/listof.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lm.influence.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lm.summaries.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lmfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/loadings.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/loess.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/loess.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/logLik.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/loglin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lowess.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ls.diag.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ls.print.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/lsfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/mad.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/mahalanobis.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/make.link.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/makepredictcall.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/manova.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/mantelhaen.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/mauchly.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/mcnemar.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/median.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/medpolish.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/model.extract.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/model.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/model.matrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/model.tables.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/monthplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/mood.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/na.action.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/na.contiguous.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/na.fail.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nafns.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/naprint.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nextn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nlm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nlminb.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nls.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/nobs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/numericDeriv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/offset.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/oneway.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/optim.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/optimize.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/order.dendrogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/p.adjust.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/pairwise.prop.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/pairwise.t.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/pairwise.table.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/pairwise.wilcox.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.HoltWinters.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.acf.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.density.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.isoreg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.lm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.ppr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.profile.nls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.spec.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.stepfun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/plot.ts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/poisson.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/poly.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/power.anova.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/power.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/power.prop.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/power.t.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/pp.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ppoints.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ppr.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/prcomp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.HoltWinters.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.arima.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.lm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.loess.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.nls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/predict.smooth.spline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/preplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/princomp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/print.power.htest.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/print.ts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/printCoefmat.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/profile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/profile.nls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/proj.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/prop.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/prop.trend.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/qqnorm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/quade.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/quantile.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/r2dtable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/rWishart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/read.ftable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/rect.hclust.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/relevel.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/reorder.dendrogram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/reorder.factor.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/replications.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/reshape.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/residuals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/runmed.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/scatter.smooth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/screeplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/sd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/se.contrast.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/selfStart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/setNames.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/shapiro.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/sigma.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/simulate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/smooth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/smooth.spline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/smoothEnds.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/sortedXyData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/spec.ar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/spec.pgram.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/spec.taper.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/spectrum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/splinefun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/start.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stat.anova.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stats-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stats-deprecated.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stats-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/step.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stepfun.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/stlmethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/summary.aov.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/summary.glm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/summary.lm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/summary.manova.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/summary.nls.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/summary.princomp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/supsmu.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/symnum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/t.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/termplot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/terms.formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/terms.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/terms.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/time.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/toeplitz.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ts-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ts.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ts.plot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/ts.union.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/tsSmooth.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/tsdiag.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/tsp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/uniroot.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/update.formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/update.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/var.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/varimax.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/vcov.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/weighted.mean.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/weighted.residuals.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/weights.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/wilcox.test.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/window.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/xtabs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/html/zC.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/coef-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/confint-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/logLik-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/mle-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/mle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/plot-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/profile-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/profile.mle-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/show-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/stats4-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/summary-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/summary.mle-class.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/update-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats4/html/vcov-methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/Surv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/Surv2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/Surv2data.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/Survmethods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/aareg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/aeqSurv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/aggregate.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/agreg.fit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/aml.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/anova.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/attrassign.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/basehaz.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/bladder.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/blogit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/cch.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/cgd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/cgd0.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/cipoisson.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/clogit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/cluster.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/colon.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/concordance.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/concordancefit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/cox.zph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/coxph.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/coxph.detail.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/coxph.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/coxph.wtest.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/coxsurv.fit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/diabetic.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/dsurvreg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/finegray.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/flchain.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/frailty.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/gbsg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/heart.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/is.ratetable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/kidney.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/levels.Surv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/lines.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/logLik.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/logan.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/lung.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/mgus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/mgus2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/model.frame.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/model.matrix.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/myeloid.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/nafld.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/neardate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/nsk.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/nwtco.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/ovarian.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/pbc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/pbcseq.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/plot.aareg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/plot.cox.zph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/plot.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/predict.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/predict.survreg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/print.aareg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/print.summary.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/print.summary.survexp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/print.summary.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/print.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/pseudo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/pspline.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/pyears.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/quantile.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/ratetable.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/ratetableDate.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/rats.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/rats2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/reliability.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/residuals.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/residuals.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/residuals.survreg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/retinopathy.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/rhDNase.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/ridge.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/rotterdam.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/royston.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/rttright.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/solder.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/stanford2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/statefig.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/strata.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/summary.aareg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/summary.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/summary.pyears.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/summary.survexp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/summary.survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survSplit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survcheck.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survdiff.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survexp.fit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survexp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survexp.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survexp.us.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfit.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfit.formula.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfit.matrix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfit.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfit0.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survfitcoxph.fit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survival-deprecated.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survival-internal.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survobrien.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survreg.control.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survreg.distributions.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survreg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survreg.object.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/survregDtest.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/tcut.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/tmerge.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/tobin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/transplant.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/udca.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/untangle.specials.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/uspop2.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/vcov.coxph.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/veteran.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/xtfrm.Surv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/yates.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/html/yates_setup.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/TclInterface.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/TkCommands.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/TkWidgetcmds.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/TkWidgets.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tclServiceMode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tcltk-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tcltk-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tkProgressBar.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tkStartGUI.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tk_choose.dir.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tk_choose.files.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tk_messageBox.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tk_select.list.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tcltk/html/tkpager.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/CRANtools.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/HTMLheader.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/HTMLlinks.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/QC.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/Rcmd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/Rd2HTML.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/Rd2txt_options.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/RdTextFilter.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/Rdiff.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/Rdindex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/Rdutils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/SweaveTeXFilter.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/add_datalist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/assertCondition.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/bibstyle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/buildVignette.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/buildVignettes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/charsets.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkFF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkMD5sums.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkPoFiles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkRd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkRdaFiles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkTnF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/checkVignettes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/check_packages_in_dir.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/codoc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/compactPDF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/delimMatch.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/dependsOnPkgs.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/encoded.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/fileutils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/find_gs_cmd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/getVignetteInfo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/loadRdMacros.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/makeLazyLoading.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/make_translations_pkg.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/makevars.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/md5sum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/package_dependencies.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/package_native_routine_registration_skeleton.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/parseLatex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/parse_Rd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/print.via.format.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/pskill.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/psnice.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/read.00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/showNonASCII.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/startDynamicHelp.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/testInstalledPackage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/texi2dvi.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/toHTML.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/toRd.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/toTitleCase.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/tools-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/tools-deprecated.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/tools-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/undoc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/updatePACKAGES.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/update_pkg_po.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/userdir.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/vignetteEngine.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/vignetteInfo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/writePACKAGES.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/tools/html/xgettext.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/00Index.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/BATCH.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/COMPILE.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/DLL.version.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/INSTALL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/LINK.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/PkgUtils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Question.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/REMOVE.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/RHOME.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/RShowDoc.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/RSiteSearch.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Rconsole.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Rprof.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Rprofmem.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Rscript.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Rtangle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/RweaveLatex.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/SHLIB.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/Sweave.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/SweaveSyntConv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/SweaveUtils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/URLencode.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/View.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/adist.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/alarm.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/apropos.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/aregexec.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/arrangeWindows.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/askYesNo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/aspell-utils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/aspell.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/available.packages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/bibentry.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/browseEnv.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/browseURL.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/browseVignettes.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/bug.report.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/capture.output.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/changedFiles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/charClass.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/choose.dir.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/choose.files.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/chooseBioCmirror.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/chooseCRANmirror.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/citEntry.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/citation.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/cite.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/clipboard.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/close.socket.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/combn.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/compareVersion.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/contrib.url.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/count.fields.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/create.post.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/data.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/dataentry.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/debugcall.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/debugger.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/demo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/download.file.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/download.packages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/edit.data.frame.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/edit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/example.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/file.edit.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/filetest.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/findLineNum.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/fix.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/flush.console.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/format.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/getAnywhere.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/getFromNamespace.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/getParseData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/getS3method.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/getWindowsHandle.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/getWindowsHandles.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/glob2rx.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/globalVariables.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/hasName.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/head.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/help.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/help.request.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/help.search.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/help.start.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/hsearch-utils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/install.packages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/installed.packages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/isS3method.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/isS3stdGen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/localeToCharset.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/ls_str.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/maintainer.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/make.packages.html.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/make.socket.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/memory.size.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/menu.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/methods.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/mirrorAdmin.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/modifyList.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/news.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/nsl.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/object.size.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/package.skeleton.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/packageDescription.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/packageName.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/packageStatus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/page.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/process.events.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/prompt.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/promptData.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/promptPackage.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/rcompgen.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/read.DIF.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/read.fortran.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/readRegistry.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/roman.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/select.list.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/sessionInfo.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/shortPathName.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/sourceutils.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/str.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/type.convert.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/unzip.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/update.packages.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/utils-defunct.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/utils-package.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/vignette.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/winDialog.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/winMenus.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
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+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/winextras.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/write.table.html
+ for i in $RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R|g' /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/html/zip.html
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~/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R ~/build/BUILD/R-4.1.0
+ pushd /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R
+ ln -s ../../include/R include
+ popd
~/build/BUILD/R-4.1.0
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+ pushd /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/texmf/tex/latex
~/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/texmf/tex/latex ~/build/BUILD/R-4.1.0
+ ln -s /usr/share/R/texmf/tex/latex R
+ popd
~/build/BUILD/R-4.1.0
+ /usr/bin/find-debuginfo -j6 --strict-build-id -m -i --build-id-seed 4.1.0-1.eln112 --unique-debug-suffix -4.1.0-1.eln112.x86_64 --unique-debug-src-base R-4.1.0-1.eln112.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/R-4.1.0
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/bin/exec/R
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/bin/Rscript
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/bin/Rscript
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/KernSmooth/libs/KernSmooth.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/lib/libR.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/MASS/libs/MASS.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/Matrix/libs/Matrix.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/class/libs/class.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/cluster/libs/cluster.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/foreign/libs/foreign.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grDevices/libs/cairo.so
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extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/graphics/libs/graphics.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/grid/libs/grid.so
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extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/methods/libs/methods.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/mgcv/libs/mgcv.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nlme/libs/nlme.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/nnet/libs/nnet.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/parallel/libs/parallel.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/rpart/libs/rpart.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/spatial/libs/spatial.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/splines/libs/splines.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/stats/libs/stats.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/survival/libs/survival.so
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extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/library/utils/libs/utils.so
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extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/modules/R_de.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/modules/internet.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/modules/lapack.so
extracting debug info from /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/libRmath.so
original debug info size: 22044kB, size after compression: 20640kB
/usr/bin/sepdebugcrcfix: Updated 33 CRC32s, 0 CRC32s did match.
19815 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/bin/true
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.D5TLFk
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-4.1.0
+ ulimit -s 16384
+ TZ=Europe/Paris
+ make check
make[1]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests/Examples'
Testing examples for package 'base'
Testing examples for package 'tools'
  comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
Testing examples for package 'grDevices'
  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
  comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
  comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE
  393,394d392
  < Warning in HoltWinters(co2) :
  <   optimization difficulties: ERROR: ABNORMAL_TERMINATION_IN_LNSRCH
  12734,12735d12731
  < Warning in HoltWinters(co2) :
  <   optimization difficulties: ERROR: ABNORMAL_TERMINATION_IN_LNSRCH
Testing examples for package 'datasets'
  comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
Testing examples for package 'grid'
  comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
  comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
  comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
Testing examples for package 'compiler'
Testing examples for package 'parallel'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests/Examples'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running strict specific tests
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running code in 'eval-etc.R' ... OK
  comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
  comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
  comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
  comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
  comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
  comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
  comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'any-all.R' ... OK
  comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
  comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
running sloppy specific tests
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running code in 'complex.R' ... OK
  comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'eval-etc-2.R' ... OK
  comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ... OK
running code in 'print-tests.R' ... OK
  comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK
running code in 'lapack.R' ... OK
  comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
  comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
  comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
  comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
checking Sys.timezone ...
make[4]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running code in 'timezone.R' ... OK
make[4]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running regression tests ...
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running code in 'array-subset.R' ... OK
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-1d.R' ... OK
running code in 'reg-tests-2.R' ... OK
  comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'd-p-q-r-tst-2.R' ... OK
running code in 'r-strict-tst.R' ... OK
running code in 'reg-IO.R' ... OK
  comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
  comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
  comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4-examples.R' ... OK
running code in 'reg-BLAS.R' ... OK
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running code in 'reg-tests-3.R' ... OK
  comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ...882,885c882
< [1] FALSE
< Warning message:
< In Sys.setlocale("LC_CTYPE", mbyte.lc) :
<   OS reports request to set locale to "en_US.UTF-8" cannot be honored
---
> [1] TRUE
 OK
running code in 'reg-examples3.R' ... OK
  comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK
running tests of plotting Latin-1
  expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
running code in 'reg-S4.R' ... OK
  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running tests of Internet functions
make[3]: Entering directory '/builddir/build/BUILD/R-4.1.0/tests'
running code in 'internet.R' ... OK
  comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247
< Warning message:
< In nsl("cran.r-project.org") :
<   nsl() was unable to resolve host 'cran.r-project.org'
---
> > 
> > # test do_download (and "record" #{packages}):
> > ap <- available.packages(contrib.url("http://cran.r-project.org"))
> > ## IGNORE_RDIFF_END
> > 
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
>  [1] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
>  [2] "<html>"                                                                                                   
>  [3] "<head>"                                                                                                   
>  [4] "<title>The Comprehensive R Archive Network</title>"                                                       
>  [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"                                  
>  [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                           
>  [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                  
>  [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"                                               
>  [9] "</head>"                                                                                                  
> [10] ""                                                                                                         
> [11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">"                                                       
> [12] "<FRAMESET rows=\"120, 1*\">"                                                                              
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"                                                    
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"                                              
> [15] "</FRAMESET>"                                                                                              
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"                                               
> [17] "<noframes>"                                                                                               
> [18] "<h1>The Comprehensive R Archive Network</h1>"                                                             
> [19] ""                                                                                                         
> [20] "Your browser seems not to support frames,"                                                                
> [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN."                                           
> [22] "</noframes>"                                                                                              
> [23] "</FRAMESET>"                                                                                              
> > close(zz)
> > 
> > # and via read.table, test http and ftp.
> > 
> > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > 
 OK
make[3]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[2]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
make[1]: Leaving directory '/builddir/build/BUILD/R-4.1.0/tests'
Processing files: R-4.1.0-1.eln112.x86_64
Processing files: R-core-4.1.0-1.eln112.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
warning: Duplicate build-ids /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/bin/Rscript and /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib64/R/bin/Rscript
warning: absolute symlink: /usr/share/texmf/tex/latex/R -> /usr/share/R/texmf/tex/latex
Provides: R(ABI) = 4.1 R(KernSmooth) = 2.23.20 R(MASS) = 7.3.54 R(Matrix) = 1.3.3 R(base) = 4.1.0 R(boot) = 1.3.28 R(class) = 7.3.19 R(cluster) = 2.1.2 R(codetools) = 0.2.18 R(compiler) = 4.1.0 R(datasets) = 4.1.0 R(foreign) = 0.8.81 R(grDevices) = 4.1.0 R(graphics) = 4.1.0 R(grid) = 4.1.0 R(lattice) = 0.20.44 R(methods) = 4.1.0 R(mgcv) = 1.8.35 R(nlme) = 3.1.152 R(nnet) = 7.3.16 R(parallel) = 4.1.0 R(rpart) = 4.1.15 R(spatial) = 7.3.14 R(splines) = 4.1.0 R(stats) = 4.1.0 R(stats4) = 4.1.0 R(survival) = 3.2.11 R(tcltk) = 4.1.0 R(tools) = 4.1.0 R(translations) = 4.1.0 R(utils) = 4.1.0 R-KernSmooth = 2.23.20 R-MASS = 7.3.54 R-Matrix = 1.3.3 R-base = 4.1.0 R-boot = 1.3.28 R-class = 7.3.19 R-cluster = 2.1.2 R-codetools = 0.2.18 R-compiler = 4.1.0 R-core = 4.1.0-1.eln112 R-core(x86-64) = 4.1.0-1.eln112 R-datasets = 4.1.0 R-foreign = 0.8.81 R-grDevices = 4.1.0 R-graphics = 4.1.0 R-grid = 4.1.0 R-lattice = 0.20.44 R-methods = 4.1.0 R-mgcv = 1.8.35 R-nlme = 3.1.152 R-nnet = 7.3.16 R-parallel = 4.1.0 R-rpart = 4.1.15 R-spatial = 7.3.14 R-splines = 4.1.0 R-stats = 4.1.0 R-stats4 = 4.1.0 R-survival = 3.2.11 R-tcltk = 4.1.0 R-tools = 4.1.0 R-translations = 4.1.0 R-utils = 4.1.0 config(R-core) = 4.1.0-1.eln112 libR.so()(64bit)
Requires(interp): /bin/sh /bin/sh /bin/sh
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /bin/sh
Requires(postun): /bin/sh
Requires(posttrans): /bin/sh
Requires: /bin/sh glibc >= 2.33.9000-50.eln112 ld-linux-x86-64.so.2()(64bit) ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit) libR.so()(64bit) libX11.so.6()(64bit) libXmu.so.6()(64bit) libXt.so.6()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.16)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libcairo.so.2()(64bit) libcurl.so.4()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgobject-2.0.so.0()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libicui18n.so.69()(64bit) libicuuc.so.69()(64bit) libjpeg.so.62()(64bit) libjpeg.so.62(LIBJPEG_6.2)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libopenblas.so.0()(64bit) libpango-1.0.so.0()(64bit) libpangocairo-1.0.so.0()(64bit) libpcre2-8.so.0()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libreadline.so.8()(64bit) libtcl8.6.so()(64bit) libtiff.so.5()(64bit) libtiff.so.5(LIBTIFF_4.0)(64bit) libtk8.6.so()(64bit) libtre.so.5()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Obsoletes: R-Matrix < 0.999375-7
Recommends: cups
Processing files: R-core-devel-4.1.0-1.eln112.x86_64
Provides: R-Matrix-devel = 1.3.3 R-core-devel = 4.1.0-1.eln112 R-core-devel(x86-64) = 4.1.0-1.eln112 pkgconfig(libR) = 4.1.0
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config
Obsoletes: R-Matrix-devel < 0.999375-7
Processing files: R-devel-4.1.0-1.eln112.x86_64
Processing files: R-java-4.1.0-1.eln112.x86_64
Processing files: R-java-devel-4.1.0-1.eln112.x86_64
Processing files: libRmath-4.1.0-1.eln112.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ZjGN0O
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-4.1.0
+ DOCDIR=/builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/libRmath
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/libRmath
+ cp -pr doc/COPYING /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/share/doc/libRmath
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: libRmath = 4.1.0-1.eln112 libRmath(x86-64) = 4.1.0-1.eln112 libRmath.so()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH)
Processing files: libRmath-devel-4.1.0-1.eln112.x86_64
Provides: libRmath-devel = 4.1.0-1.eln112 libRmath-devel(x86-64) = 4.1.0-1.eln112 pkgconfig(libRmath) = 4.1.0
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config
Processing files: libRmath-static-4.1.0-1.eln112.x86_64
Provides: libRmath-static = 4.1.0-1.eln112 libRmath-static(x86-64) = 4.1.0-1.eln112
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-debugsource-4.1.0-1.eln112.x86_64
Provides: R-debugsource = 4.1.0-1.eln112 R-debugsource(x86-64) = 4.1.0-1.eln112
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-debuginfo-4.1.0-1.eln112.x86_64
Provides: R-debuginfo = 4.1.0-1.eln112 R-debuginfo(x86-64) = 4.1.0-1.eln112
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-debugsource(x86-64) = 4.1.0-1.eln112
Processing files: R-core-debuginfo-4.1.0-1.eln112.x86_64
warning: Duplicate build-ids /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib/debug/usr/bin/Rscript-4.1.0-1.eln112.x86_64.debug and /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64/usr/lib/debug/usr/lib64/R/bin/Rscript-4.1.0-1.eln112.x86_64.debug
Provides: R-core-debuginfo = 4.1.0-1.eln112 R-core-debuginfo(x86-64) = 4.1.0-1.eln112 debuginfo(build-id) = 05ab43ab7a105633016409ccbf9950b1a0fcfe0f debuginfo(build-id) = 167dffafc70def4937a84ea0dad03676150d7990 debuginfo(build-id) = 1cbf689f43bdc33fc6c6717e63665987e03527fe debuginfo(build-id) = 1d91e729204a1e76b692d19235d82b7d4a7383a3 debuginfo(build-id) = 253df27f5f85e03958cc5afd930045a859796c45 debuginfo(build-id) = 2890407c0c5c76e7753db228315b71e57ad3740f debuginfo(build-id) = 2de3c2dc0777295dfe5115af9718309ab2810399 debuginfo(build-id) = 2e223b80810483e5865670216aa5633fbf29dcac debuginfo(build-id) = 3479cf9ead698bcc380deae4c7c028bd4fe683b5 debuginfo(build-id) = 3bb6f854766f6fc7d061b9f3bffaf910c9d62e04 debuginfo(build-id) = 42e0f028b5322e841d46a8b3d6674322fd08edc7 debuginfo(build-id) = 49fe9a723ecf3905007415e35e865d10d5d9663f debuginfo(build-id) = 4f0f8e6de3758ea272ff2fdb11539e9732736d60 debuginfo(build-id) = 5a784dfaa392b197a13536b5a8f79f52a8dc1c47 debuginfo(build-id) = 6474d5fd121ca2042896cfd572bfc2f56bb7569e debuginfo(build-id) = 67ea45f73d4716eeb5d7d2b88136086db70acf68 debuginfo(build-id) = 7d513674716ad0e1d3eec7f61f8d2e327bffe50e debuginfo(build-id) = 804458f85d72ed15a8aa2e168446d93497ed31fa debuginfo(build-id) = 8608ec67879b940a8a48eeca16a7c9204f5ac68a debuginfo(build-id) = 88c2854c71ef7192ef06d610dd07495f80d0fed0 debuginfo(build-id) = 8d94cc130d3d35e98befa0bf4e49ee5d53a2773d debuginfo(build-id) = 8e4f005614fa50d6fd6ff232dbe7a130a2d85916 debuginfo(build-id) = 9b770c5252d4bfee28eb27c20819af809cd7ac69 debuginfo(build-id) = aaa3f932e95f6591b5e8deec19522c5276606bb5 debuginfo(build-id) = c1fee6a3193a4df61b16ee931e393411f50ab999 debuginfo(build-id) = c51a91208a9f743d2f6f4f23c3229e6cd64a96d0 debuginfo(build-id) = d0a6516c0740d5076c3618c09bcd42a76b5fa85d debuginfo(build-id) = d5ccd9a01bb341150dcc9263439679baaba15ce1 debuginfo(build-id) = da7c15d48e3996780d8f554d549f07bbdf98a1eb debuginfo(build-id) = e975ab8aeb5a02118a354359280b242b1eb28582 debuginfo(build-id) = eaf2ef4ffbdb87ecf6e2f822c701535652352778 debuginfo(build-id) = nilnil libR.so-4.1.0-1.eln112.x86_64.debug()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-debugsource(x86-64) = 4.1.0-1.eln112
Processing files: libRmath-debuginfo-4.1.0-1.eln112.x86_64
Provides: debuginfo(build-id) = 885f3214308c32074d9c262cac63d9fe0eae1559 libRmath-debuginfo = 4.1.0-1.eln112 libRmath-debuginfo(x86-64) = 4.1.0-1.eln112 libRmath.so-4.1.0-1.eln112.x86_64.debug()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-debugsource(x86-64) = 4.1.0-1.eln112
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64
Wrote: /builddir/build/RPMS/R-core-devel-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/libRmath-debuginfo-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-debuginfo-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/libRmath-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/libRmath-devel-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-devel-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-java-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-java-devel-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/libRmath-static-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-debugsource-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-core-debuginfo-4.1.0-1.eln112.x86_64.rpm
Wrote: /builddir/build/RPMS/R-core-4.1.0-1.eln112.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.hzgscV
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-4.1.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-4.1.0-1.eln112.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0