Mock Version: 1.3.4
Mock Version: 1.3.4
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64 --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/epel7-build-12419316-909796/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': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fff869f1f98>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64 --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': 'en_US.UTF-8'} and shell False
Building target platforms: ppc64
Building for target ppc64
Wrote: /builddir/build/SRPMS/R-3.5.0-1.el7.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64 --nodeps /builddir/build/SPECS/R.spec'], chrootPath='/var/lib/mock/epel7-build-12419316-909796/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': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fff869f1f98>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64 --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': 'en_US.UTF-8'} and shell False
Building target platforms: ppc64
Building for target ppc64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jXGxQa
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf R-3.5.0
+ /usr/bin/gzip -dc /builddir/build/SOURCES/R-3.5.0.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd R-3.5.0
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):'
Patch #1 (R-3.3.0-fix-java_path-in-javareconf.patch):
+ /usr/bin/patch -p1 -b --suffix .fixpath --fuzz=0
+ /usr/bin/cat /builddir/build/SOURCES/R-3.3.0-fix-java_path-in-javareconf.patch
patching file src/scripts/javareconf.in
Hunk #1 succeeded at 79 (offset 1 line).
+ cat
+ chmod +x /builddir/build/BUILD/R-3.5.0/R-prov
+ cat
+ chmod +x /builddir/build/BUILD/R-3.5.0/R-req
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.n7p9W0
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.5.0
+ echo 'R_LIBS_SITE=${R_LIBS_SITE-'\''/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library'\''}'
+ export R_RD4PDF=times,hyper
+ R_RD4PDF=times,hyper
+ sed -i 's|inconsolata,||g' etc/Renviron.in
+ export R_PDFVIEWER=/usr/bin/xdg-open
+ R_PDFVIEWER=/usr/bin/xdg-open
+ export R_PRINTCMD=lpr
+ R_PRINTCMD=lpr
+ export R_BROWSER=/usr/bin/xdg-open
+ R_BROWSER=/usr/bin/xdg-open
+ case "ppc64" in
+ export 'CC=gcc -m64'
+ CC='gcc -m64'
+ export 'CXX=g++ -m64'
+ CXX='g++ -m64'
+ export 'F77=gfortran -m64'
+ F77='gfortran -m64'
+ export 'FC=gfortran -m64'
+ FC='gfortran -m64'
+ export 'FCFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7'
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7'
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro '
+ export LDFLAGS
+ '[' 1 == 1 ']'
+ '[' ppc64 == ppc64le ']'
++ find . -name config.guess -o -name config.sub
+ for i in '$(find . -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
+ for i in '$(find . -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
+ ./configure --build=ppc64-redhat-linux-gnu --host=ppc64-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-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh --enable-BLAS-shlib --enable-R-shlib --enable-prebuilt-html MAKEINFO=texi2any rdocdir=/usr/share/doc/R-3.5.0 rincludedir=/usr/include/R rsharedir=/usr/share/R
configure: WARNING: unrecognized options: --disable-dependency-tracking
./configure: line 27483: ::: command not found
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ cat CONFIGURE.log
+ grep -A30 'R is now' -
+ make V=1
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/m4'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/tools'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/tools'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/doc'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/doc/html'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/doc/html'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
make[2]: Nothing to be done for `R'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/doc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/etc'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/etc'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/share'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/share'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/scripts'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/scripts'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/include'
mkdir -p -- ../../include
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/include/R_ext'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/include'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra/blas'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra/blas'
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c blas.f -o blas.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
blas.f: In function 'drotmg':
blas.f:1614:0: warning: 'dh22' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH22=DH22*GAM
 ^
blas.f:1613:0: warning: 'dh21' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH21=DH21*GAM
 ^
blas.f:1591:0: warning: 'dh12' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH12=DH12*GAM
 ^
blas.f:1590:0: warning: 'dh11' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DH11=DH11*GAM
 ^
blas.f: In function 'dspr':
blas.f:2409:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
blas.f: In function 'dspr2':
blas.f:2697:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
                      AP( K ) = AP( K ) + X( IX )*TEMP1 + Y( IY )*TEMP2
 ^
blas.f:2697:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f:2618:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, K, KK, KX, KY
 ^
blas.f:2618:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f: In function 'dsyr':
blas.f:3451:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
blas.f: In function 'dsyr2':
blas.f:3740:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                                     + Y( IY )*TEMP2
 ^
blas.f:3740:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
blas.f:3765:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( ( X( JX ).NE.ZERO ).OR.( Y( JY ).NE.ZERO ) )THEN
 ^
blas.f:3659:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, KX, KY
 ^
blas.f: In function 'dtbmv':
blas.f:4729:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   TEMP = X( JX )
 ^
blas.f: In function 'dtbsv':
blas.f:5043:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   TEMP = X( JX )
 ^
blas.f: In function 'dtpmv':
blas.f:5375:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   TEMP = X( JX )
 ^
blas.f: In function 'dtpsv':
blas.f:5608:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   IF( X( JX ).NE.ZERO )THEN
 ^
blas.f: In function 'dtrmv':
blas.f:6319:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   TEMP = X( JX )
 ^
blas.f: In function 'dtrsv':
blas.f:6927:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   IF( X( JX ).NE.ZERO )THEN
 ^
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c cmplxblas.f -o cmplxblas.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
cmplxblas.f:4796.26:
                  RTEMP = RTEMP + DCONJG( A( L, J ) )*A( L, J )         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplxblas.f:4808.26:
                  RTEMP = RTEMP + DCONJG( A( L, J ) )*A( L, J )         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplxblas.f: In function 'zher2':
cmplxblas.f:1130:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, KX, KY
 ^
cmplxblas.f:1130:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:1130:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:1130:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f: In function 'ztrmv':
cmplxblas.f:2208:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplxblas.f: In function 'ztrsv':
cmplxblas.f:2946:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplxblas.f: In function 'zher':
cmplxblas.f:4386:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplxblas.f: In function 'zhpr':
cmplxblas.f:5195:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
cmplxblas.f: In function 'zhpr2':
cmplxblas.f:5423:0: warning: 'ky' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, IY, J, JX, JY, K, KK, KX, KY
 ^
cmplxblas.f:5423:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:5423:0: warning: 'jy' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f:5423:0: warning: 'jx' may be used uninitialized in this function [-Wmaybe-uninitialized]
cmplxblas.f: In function 'ztbmv':
cmplxblas.f:6649:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KPLUS1, KX, L
 ^
cmplxblas.f: In function 'ztbsv':
cmplxblas.f:7030:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KPLUS1, KX, L
 ^
cmplxblas.f: In function 'ztpmv':
cmplxblas.f:7367:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
cmplxblas.f: In function 'ztpsv':
cmplxblas.f:7708:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, K, KK, KX
 ^
gcc -m64 -std=gnu99 -shared -fopenmp -Wl,-z,relro  -o libRblas.so blas.o  cmplxblas.o -lgfortran -lm
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/extra/blas'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra/blas'
mkdir -p -- /builddir/build/BUILD/R-3.5.0/lib
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/extra/blas'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/extra/blas'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/extra'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/appl'
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c integrate.c -o integrate.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c interv.c -o interv.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c maxcol.c -o maxcol.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c optim.c -o optim.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pretty.c -o pretty.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c uncmin.c -o uncmin.o
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dchdc.f -o dchdc.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dpbfa.f -o dpbfa.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dpbsl.f -o dpbsl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dpoco.f -o dpoco.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dpodi.f -o dpodi.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dpofa.f -o dpofa.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dposl.f -o dposl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dqrdc.f -o dqrdc.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dqrdc2.f -o dqrdc2.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dqrls.f -o dqrls.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dqrsl.f -o dqrsl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dqrutl.f -o dqrutl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dsvdc.f -o dsvdc.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dtrco.f -o dtrco.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dtrsl.f -o dtrsl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
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-3.5.0/src/appl'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/appl'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/nmath'
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mlutils.c -o mlutils.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c d1mach.c -o d1mach.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c i1mach.c -o i1mach.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fmax2.c -o fmax2.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fmin2.c -o fmin2.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fprec.c -o fprec.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fround.c -o fround.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ftrunc.c -o ftrunc.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sign.c -o sign.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fsign.c -o fsign.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c imax2.c -o imax2.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c imin2.c -o imin2.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chebyshev.c -o chebyshev.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c log1p.c -o log1p.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgammacor.c -o lgammacor.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gammalims.c -o gammalims.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stirlerr.c -o stirlerr.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bd0.c -o bd0.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gamma.c -o gamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgamma.c -o lgamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gamma_cody.c -o gamma_cody.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c beta.c -o beta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lbeta.c -o lbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c polygamma.c -o polygamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cospi.c -o cospi.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_i.c -o bessel_i.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_j.c -o bessel_j.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_k.c -o bessel_k.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_y.c -o bessel_y.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c choose.c -o choose.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c snorm.c -o snorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sexp.c -o sexp.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgamma.c -o dgamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pgamma.c -o pgamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qgamma.c -o qgamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rgamma.c -o rgamma.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbeta.c -o dbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pbeta.c -o pbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qbeta.c -o qbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbeta.c -o rbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dunif.c -o dunif.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c punif.c -o punif.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qunif.c -o qunif.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c runif.c -o runif.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnorm.c -o dnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnorm.c -o pnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnorm.c -o qnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnorm.c -o rnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dlnorm.c -o dlnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plnorm.c -o plnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qlnorm.c -o qlnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlnorm.c -o rlnorm.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c df.c -o df.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pf.c -o pf.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qf.c -o qf.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rf.c -o rf.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnf.c -o dnf.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dt.c -o dt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pt.c -o pt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qt.c -o qt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rt.c -o rt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnt.c -o dnt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dchisq.c -o dchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pchisq.c -o pchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qchisq.c -o qchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rchisq.c -o rchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnchisq.c -o rnchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbinom.c -o dbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pbinom.c -o pbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qbinom.c -o qbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbinom.c -o rbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rmultinom.c -o rmultinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dcauchy.c -o dcauchy.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pcauchy.c -o pcauchy.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qcauchy.c -o qcauchy.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rcauchy.c -o rcauchy.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dexp.c -o dexp.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pexp.c -o pexp.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qexp.c -o qexp.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rexp.c -o rexp.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgeom.c -o dgeom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pgeom.c -o pgeom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qgeom.c -o qgeom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rgeom.c -o rgeom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dhyper.c -o dhyper.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c phyper.c -o phyper.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qhyper.c -o qhyper.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rhyper.c -o rhyper.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnbinom.c -o dnbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnbinom.c -o pnbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnbinom.c -o qnbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnbinom.c -o rnbinom.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dpois.c -o dpois.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ppois.c -o ppois.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qpois.c -o qpois.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpois.c -o rpois.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dweibull.c -o dweibull.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pweibull.c -o pweibull.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qweibull.c -o qweibull.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rweibull.c -o rweibull.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dlogis.c -o dlogis.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plogis.c -o plogis.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qlogis.c -o qlogis.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlogis.c -o rlogis.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnchisq.c -o dnchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnchisq.c -o pnchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnchisq.c -o qnchisq.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnbeta.c -o dnbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnbeta.c -o pnbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnbeta.c -o qnbeta.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnf.c -o pnf.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnt.c -o pnt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnf.c -o qnf.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnt.c -o qnt.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ptukey.c -o ptukey.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qtukey.c -o qtukey.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c toms708.c -o toms708.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c wilcox.c -o wilcox.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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-3.5.0/src/nmath'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/nmath'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/unix'
config.status: creating src/unix/Makefile
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/unix'
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-3.5.0/src/unix'
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Rembedded.c -o Rembedded.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dynload.c -o dynload.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c system.c -o system.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sys-unix.c -o sys-unix.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sys-std.c -o sys-std.o
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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-3.5.0/src/unix'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/unix'
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -Wl,-z,relro  -DR_HOME='"/builddir/build/BUILD/R-3.5.0"' \
  -o Rscript ./Rscript.c
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/unix'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
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 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 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-3.5.0/src/main'
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c CommandLineArgs.c -o CommandLineArgs.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Rdynload.c -o Rdynload.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Renviron.c -o Renviron.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c RNG.c -o RNG.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agrep.c -o agrep.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c altrep.c -o altrep.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c apply.c -o apply.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c arithmetic.c -o arithmetic.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c array.c -o array.o
array.c: In function 'mayHaveNaNOrInf_simd':
array.c:651:0: warning: ignoring #pragma omp simd [-Wunknown-pragmas]
     #pragma omp simd reduction(+:s)
 ^
array.c: In function 'cmayHaveNaNOrInf_simd':
array.c:677:0: warning: ignoring #pragma omp simd [-Wunknown-pragmas]
     #pragma omp simd reduction(+:s)
 ^
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c attrib.c -o attrib.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bind.c -o bind.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c builtin.c -o builtin.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c character.c -o character.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coerce.c -o coerce.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c colors.c -o colors.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c complex.c -o complex.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c connections.c -o connections.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c context.c -o context.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cum.c -o cum.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dcf.c -o dcf.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c datetime.c -o datetime.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c debug.c -o debug.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c deparse.c -o deparse.o
deparse.c: In function 'deparse2buff':
deparse.c:1434:8: warning: 'doquote' may be used uninitialized in this function [-Wmaybe-uninitialized]
      if(doquote)
        ^
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devices.c -o devices.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dotcode.c -o dotcode.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dounzip.c -o dounzip.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dstruct.c -o dstruct.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c duplicate.c -o duplicate.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c edit.c -o edit.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c engine.c -o engine.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c envir.c -o envir.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c errors.c -o errors.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c eval.c -o eval.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c format.c -o format.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gevents.c -o gevents.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gram.c -o gram.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gram-ex.c -o gram-ex.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c graphics.c -o graphics.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c grep.c -o grep.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c identical.c -o identical.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c inlined.c -o inlined.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c inspect.c -o inspect.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c internet.c -o internet.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c iosupport.c -o iosupport.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lapack.c -o lapack.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c list.c -o list.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c localecharset.c -o localecharset.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c logic.c -o logic.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c main.c -o main.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mapply.c -o mapply.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c match.c -o match.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c memory.c -o memory.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c names.c -o names.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c objects.c -o objects.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c options.c -o options.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c paste.c -o paste.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c platform.c -o platform.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plot.c -o plot.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plot3d.c -o plot3d.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plotmath.c -o plotmath.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c print.c -o print.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c printarray.c -o printarray.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c printvector.c -o printvector.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c printutils.c -o printutils.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qsort.c -o qsort.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c radixsort.c -o radixsort.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c random.c -o random.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c raw.c -o raw.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c registration.c -o registration.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c relop.c -o relop.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlocale.c -o rlocale.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c saveload.c -o saveload.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c scan.c -o scan.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c seq.c -o seq.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c serialize.c -o serialize.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sort.c -o sort.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c source.c -o source.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c split.c -o split.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sprintf.c -o sprintf.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c startup.c -o startup.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c subassign.c -o subassign.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c subscript.c -o subscript.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c subset.c -o subset.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c summary.c -o summary.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sysutils.c -o sysutils.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c times.c -o times.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c unique.c -o unique.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c util.c -o util.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c version.c -o version.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c g_alab_her.c -o g_alab_her.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c g_cntrlify.c -o g_cntrlify.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c g_fontdb.c -o g_fontdb.o
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c g_her_glyph.c -o g_her_glyph.o
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c xxxpr.f -o xxxpr.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -shared -fopenmp -Wl,-z,relro   -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.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 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`     -L"../../lib" -lRblas -lgfortran -lm   -lreadline  -ltre -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
mkdir -p -- /builddir/build/BUILD/R-3.5.0/bin/exec
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
gcc -m64 -std=gnu99   -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Rmain.c -o Rmain.o
gcc -m64 -std=gnu99 -Wl,--export-dynamic -fopenmp  -L"../../lib" -Wl,-z,relro  -o R.bin Rmain.o  -lR -lRblas
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/modules/internet'
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c Rsock.c -o Rsock.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c internet.c -o internet.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c libcurl.c -o libcurl.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c nanoftp.c -o nanoftp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c nanohttp.c -o nanohttp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c sock.c -o sock.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7   -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -m64 -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -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-3.5.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILD/R-3.5.0/modules
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/internet'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/internet'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/internet'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
making Lapack.d from Lapack.c
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
gfortran -m64 -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules -c dlamch.f -o dlamch.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dlapack.f -o dlapack.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
SRC/iparam2stage.F:6871.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:6885.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:9161.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:9776.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16788.28:
               LWORK_DGEQRF=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16792.28:
               LWORK_DORMQR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16807.28:
               LWORK_DGEBRD=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16811.28:
               LWORK_DORMBR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:98487.18:
         LWKOPT = WORK( 1 )                                             
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16815.28:
               LWORK_DORGBR=DUM(1)                                      
                            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16839.31:
                  LWORK_DGELQF=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16843.31:
                  LWORK_DGEBRD=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16847.31:
                  LWORK_DORMBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16851.31:
                  LWORK_DORGBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16855.31:
                  LWORK_DORMLQ=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16875.31:
                  LWORK_DGEBRD=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16879.31:
                  LWORK_DORMBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:16883.31:
                  LWORK_DORGBR=DUM(1)                                   
                               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:36428.13:
      LOPT = WORK( 1 )                                                  
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:35370.13:
      LOPT = WORK( M+NP+1 )                                             
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:36726.13:
      LOPT = WORK( 1 )                                                  
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:36074.13:
      LOPT = WORK( P+MN+1 )                                             
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:124156.14:
      LWMIN = MAX( DBLE( LWMIN ), DBLE( WORK( 1 ) ) )                   
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:124157.15:
      LIWMIN = MAX( DBLE( LIWMIN ), DBLE( IWORK( 1 ) ) )                
               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:136875.13:
      LOPT = MAX( DBLE( LOPT ), DBLE( WORK( 1 ) ) )                     
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:136876.14:
      LIOPT = MAX( DBLE( LIOPT ), DBLE( IWORK( 1 ) ) )                  
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:138054.21:
            LWKOPT = WORK(1)                                            
                     1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
SRC/iparam2stage.F:77843.34:
      SUBROUTINE DLARRV( N, VL, VU, D, L, PIVMIN,                       
                                  1
Warning: Unused dummy argument 'vu' at (1)
SRC/iparam2stage.F:74326.54:
      SUBROUTINE DLARRC( JOBT, N, VL, VU, D, E, PIVMIN,                 
                                                      1
Warning: Unused dummy argument 'pivmin' at (1)
SRC/iparam2stage.F:46267.45:
     $                   RELTOL, PIVMIN, D, E, E2, NVAL, AB, C, MOUT,   
                                             1
Warning: Unused dummy argument 'e' at (1)
SRC/iparam2stage.F:58693.55:
      INTEGER FUNCTION DLANEG( N, D, LLD, SIGMA, PIVMIN, R )            
                                                       1
Warning: Unused dummy argument 'pivmin' at (1)
SRC/iparam2stage.F:612.68:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                                    1
Warning: Unused dummy argument 'lwork' at (1)
SRC/iparam2stage.F:612.51:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                   1
Warning: Unused dummy argument 'n' at (1)
SRC/iparam2stage.F:612.48:
      INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK )  
                                                1
Warning: Unused dummy argument 'opts' at (1)
SRC/iparam2stage.F:128949.23:
     $           ABSTOL, M, W, Z, LDZ, ISUPPZ, WORK, LWORK, IWORK,      
                       1
Warning: Unused dummy argument 'abstol' at (1)
dlapack.f: In function 'dlatrs':
dlapack.f:95122:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dlatps':
dlapack.f:93997:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dlatbs':
dlapack.f:92881:0: warning: 'tjjs' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   X( J ) = X( J ) / TJJS - SUMJ
 ^
dlapack.f: In function 'dsptrf':
dlapack.f:126563:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
dlapack.f: In function 'dtptri':
dlapack.f:155012:0: warning: 'jclast' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                     AP( JCLAST ), AP( JC+1 ), 1 )
 ^
dlapack.f: In function 'dlaruv':
dlapack.f:79873:0: warning: 'it4' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 4 ) = IT4
 ^
dlapack.f:79872:0: warning: 'it3' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 3 ) = IT3
 ^
dlapack.f:79871:0: warning: 'it2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 2 ) = IT2
 ^
dlapack.f:79870:0: warning: 'it1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ISEED( 1 ) = IT1
 ^
dlapack.f: In function 'dstein':
dlapack.f:129376:0: warning: 'xjm' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ABS( XJ-XJM ).GT.ORTOL )
 ^
dlapack.f:129376:0: warning: 'ortol' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:129362:0: warning: 'onenrm' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $            ABS( WORK( INDRV1+JMAX ) )
 ^
dlapack.f:129396:0: warning: 'dtpcrt' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( NRM.LT.DTPCRT )
 ^
dlapack.f: In function 'dlaed6':
dlapack.f:49708:0: warning: 'sclinv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $   TAU = TAU*SCLINV
 ^
dlapack.f: In function 'dgghrd':
dlapack.f:35771:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ )
 ^
dlapack.f: In function 'dgetc2':
dlapack.f:30048:0: warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          A( N, N ) = SMIN
 ^
dlapack.f:30029:0: warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( JPV.NE.I )
 ^
dlapack.f:30023:0: warning: 'ipv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( IPV.NE.I )
 ^
dlapack.f: In function 'dlasy2':
dlapack.f:91210:0: warning: 'jpsv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $      CALL DSWAP( 4, T16( 1, JPSV ), 1, T16( 1, I ), 1 )
 ^
dlapack.f:91204:0: warning: 'ipsv' may be used uninitialized in this function [-Wmaybe-uninitialized]
             CALL DSWAP( 4, T16( IPSV, 1 ), 4, T16( I, 1 ), 4 )
 ^
dlapack.f: In function 'dtgevc':
dlapack.f:147008:0: warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILBACK ) THEN
 ^
dlapack.f: In function 'dlasq4':
dlapack.f:88702:0: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
       TAU = S
 ^
dlapack.f: In function 'dsytf2':
dlapack.f:139620:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
dlapack.f: In function 'dlals0':
dlapack.f:57295:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                           DIFRJ ) / ( POLES( I, 2 )+DJ )
 ^
dlapack.f: In function 'dlasd8':
dlapack.f:85755:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   / ( DSIGMA( I )+DJ )
 ^
dlapack.f: In function 'dlantr':
dlapack.f:62441:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlantp':
dlapack.f:62069:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlantb':
dlapack.f:61724:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlansy':
dlapack.f:61464:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlanst':
dlapack.f:61256:0: warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ANORM, SCALE, SUM
 ^
dlapack.f: In function 'dlansp':
dlapack.f:61009:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlansb':
dlapack.f:59803:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dlahr2':
dlapack.f:55512:0: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
dlapack.f: In function 'dlaed8':
dlapack.f:50392:0: warning: 'jlam' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2
 ^
dlapack.f: In function 'dlaed2':
dlapack.f:47548:0: warning: 'pj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   N2, NJ, PJ
 ^
dlapack.f: In function 'dlahqr':
dlapack.f:55126:0: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                DO 100 J = K, I2
 ^
dlapack.f: In function 'dlasd7':
dlapack.f:85161:0: warning: 'jprev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M, N,
 ^
dlapack.f: In function 'dlasd2':
dlapack.f:82313:0: warning: 'jprev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            CT, I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M,
 ^
dlapack.f: In function 'dlanhs':
dlapack.f:59577:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
dlapack.f: In function 'dhgeqz':
dlapack.f:43147:0: warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILZ ) THEN
 ^
dlapack.f:42638:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ ) THEN
 ^
dlapack.f:42861:0: warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( .NOT.ILSCHR ) THEN
 ^
dlapack.f: In function 'dlangt':
dlapack.f:59367:0: warning: 'anorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ANORM, SCALE, SUM, TEMP
 ^
dlapack.f: In function 'dlange':
dlapack.f:59164:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
dlapack.f: In function 'dtrsen':
dlapack.f:159919:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          WORK( 1 ) = LWMIN
 ^
dlapack.f:159920:0: warning: 'liwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IWORK( 1 ) = LIWMIN
 ^
dlapack.f: In function 'dlangb':
dlapack.f:58950:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
SRC/iparam2stage.F: In function 'iparmq':
SRC/iparam2stage.F:770:0: warning: 'ns' may be used uninitialized in this function [-Wmaybe-uninitialized]
SRC/iparam2stage.F:761:0: warning: 'nh' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dlaed0':
dlapack.f:46983:0: warning: 'iwrem' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                      IWORK( SUBPBS+1 ), INFO )
 ^
dlapack.f:46983:0: warning: 'iqptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'iq' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'iprmpt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'iperm' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'igivpt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:46983:0: warning: 'igivcl' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dormql':
dlapack.f:102784:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF( NB.GT.1 .AND. NB.LT.K ) THEN
 ^
dlapack.f: In function 'dorgql':
dlapack.f:99539:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dsyevx':
dlapack.f:135615:0: warning: 'lwkopt' may be used uninitialized in this function [-Wmaybe-uninitialized]
       WORK( 1 ) = LWKOPT
 ^
dlapack.f: In function 'dlarrd':
dlapack.f:75191:0: warning: 'wul' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( W( JE ).GE.WUL .AND. IDISCU.GT.0 ) THEN
 ^
dlapack.f:75174:0: warning: 'wlu' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( W( JE ).LE.WLU .AND. IDISCL.GT.0 ) THEN
 ^
dlapack.f: In function 'dlarre':
dlapack.f:75712:0: warning: 'irange' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $       ((IRANGE.EQ.VALRNG).AND.(D(1).GT.VL).AND.(D(1).LE.VU)).OR.
 ^
dlapack.f:76205:0: warning: 'wend' may be used uninitialized in this function [-Wmaybe-uninitialized]
          WBEGIN = WEND + 1
 ^
dlapack.f:76191:0: warning: 'mb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             DO 165 I = M - MB + 1, M
 ^
dlapack.f: In function 'dormrq':
dlapack.f:104042:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( LWORK.LT.NW*NB+TSIZE ) THEN
 ^
dlapack.f: In function 'dgerqf':
dlapack.f:22115:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dtgsna':
dlapack.f:150520:0: warning: 'cond' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                           COND )
 ^
dlapack.f: In function 'dbdsdc':
dlapack.f:1544:0: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                      WORK( WSTART ), IWORK, INFO )
 ^
dlapack.f:1544:0: warning: 'poles' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'ivt' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'is' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'ic' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'givnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'givcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'difr' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:1544:0: warning: 'difl' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dormrz':
dlapack.f:104411:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF( NB.GT.1 .AND. NB.LT.K ) THEN
 ^
dlapack.f: In function 'dtzrzf':
dlapack.f:163493:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dgehrd':
dlapack.f:13098:0: warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized]
          DO 40 I = ILO, IHI - 1 - NX, NB
 ^
dlapack.f: In function 'dgbsvx':
dlapack.f:5390:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f:5405:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f: In function 'dgeesx':
dlapack.f:9704:0: warning: 'maxwrk' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   MAXWRK, MINWRK
 ^
dlapack.f: In function 'dgelss':
dlapack.f:16972:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f: In function 'dgeqlf':
dlapack.f:18898:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dgesvd':
dlapack.f:24782:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
dlapack.f:24342:0: warning: 'bdspac' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            BDSPAC, BLK, CHUNK, I, IE, IERR, IR, ISCL,
 ^
dlapack.f:24345:0: warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   NRVT, WRKBL
 ^
dlapack.f: In function 'dgesvx':
dlapack.f:29665:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f:29680:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
dlapack.f: In function 'dlahrd':
dlapack.f:55813:0: warning: 'ei' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
dlapack.f: In function 'dlansf':
dlapack.f:60141:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, S, VALUE, AA, TEMP
 ^
dlapack.f: In function 'dorcsd':
dlapack.f:97738:0: warning: 'itauq2' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IORBDB), LORBDBWORK, CHILDINFO )
 ^
dlapack.f:97738:0: warning: 'itauq1' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97738:0: warning: 'itaup2' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97738:0: warning: 'itaup1' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97802:0: warning: 'iorgqr' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   WORK(IORGQR), LORGQRWORK, INFO )
 ^
dlapack.f:97784:0: warning: 'iorglq' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   WORK(IORGLQ), LORGLQWORK, INFO )
 ^
dlapack.f:97738:0: warning: 'iorbdb' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IORBDB), LORBDBWORK, CHILDINFO )
 ^
dlapack.f:97812:0: warning: 'ibbcsd' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $             WORK(IB22E), WORK(IBBCSD), LBBCSDWORK, INFO )
 ^
dlapack.f:97812:0: warning: 'ib22e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib22d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib21e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib21d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib12e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib12d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib11e' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f:97812:0: warning: 'ib11d' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dorgrq':
dlapack.f:100327:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
dlapack.f: In function 'dpbsvx':
dlapack.f:106741:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:106741:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dposvx':
dlapack.f:110628:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:110628:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
dlapack.f: In function 'dppsvx':
dlapack.f:113309:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                SCOND = MAX( SMIN, SMLNUM ) / MIN( SMAX, BIGNUM )
 ^
dlapack.f:113309:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -m64  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c cmplx.f -o cmplx.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
cmplx.f:1780.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
cmplx.f:1794.19:
               K = SCALE( I )                                           
                   1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
cmplx.f:2456.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2475.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2500.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:2519.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21690.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21730.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21774.21:
            D( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:21808.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:3759.21:
            HSWORK = WORK( 1 )                                          
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:50903.18:
         LWKOPT = WORK( 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to INTEGER(4) at (1)
cmplx.f:18862.18:
         W( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:38115.26:
               E( I-1 ) = ALPHA                                         
                          1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:38169.24:
               E( I ) = ALPHA                                           
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19996.24:
               D( J ) = A( J, J )                                       
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19582.21:
            E( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19610.23:
            D( I+1 ) = A( I+1, I+1 )                                    
                       1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19613.18:
         D( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19626.21:
            E( I ) = ALPHA                                              
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19655.21:
            D( I ) = A( I, I )                                          
                     1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19658.18:
         D( N ) = A( N, N )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:20028.24:
               D( J ) = A( J, J )                                       
                        1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:19253.18:
         W( 1 ) = A( 1, 1 )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39333.18:
            AII = A( I, I )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39352.18:
            AII = A( I, I )                                             
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39774.18:
            AJJ = DBLE( A( J, J ) ) - ZDOTC( J-1, A( 1, J ), 1,         
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f:39801.18:
            AJJ = DBLE( A( J, J ) ) - ZDOTC( J-1, A( J, 1 ), LDA,       
                  1
Warning: Possible change of value in conversion from COMPLEX(8) to REAL(8) at (1)
cmplx.f: In function 'zsyr':
cmplx.f:42206:0: warning: 'kx' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, INFO, IX, J, JX, KX
 ^
cmplx.f: In function 'zsytf2':
cmplx.f:42910:0: warning: 'imax' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IPIV( K ) = -KP
 ^
cmplx.f: In function 'zlaed8':
cmplx.f:23865:0: warning: 'jlam' may be used uninitialized in this function [-Wmaybe-uninitialized]
       INTEGER            I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2
 ^
cmplx.f: In function 'zlantr':
cmplx.f:28016:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
cmplx.f: In function 'zlanhe':
cmplx.f:27532:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   ABSA, SCALE, SUM, VALUE
 ^
cmplx.f: In function 'ztgevc':
cmplx.f:44370:0: warning: 'ilback' may be used uninitialized in this function [-Wmaybe-uninitialized]
                IF( ILBACK ) THEN
 ^
cmplx.f:44246:0: warning: 'ilall' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILALL ) THEN
 ^
cmplx.f: In function 'zlange':
cmplx.f:27310:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE, TEMP
 ^
cmplx.f: In function 'zgetc2':
cmplx.f:14939:0: warning: 'smin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   BIGNUM, EPS, SMIN, SMLNUM, XMAX
 ^
cmplx.f:15007:0: warning: 'jpv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( JPV.NE.I )
 ^
cmplx.f:15001:0: warning: 'ipv' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( IPV.NE.I )
 ^
cmplx.f: In function 'zgghrd':
cmplx.f:18613:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ )
 ^
cmplx.f: In function 'zlanhs':
cmplx.f:27775:0: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized]
       DOUBLE PRECISION   SCALE, SUM, VALUE
 ^
cmplx.f: In function 'zhgeqz':
cmplx.f:20898:0: warning: 'ilz' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILZ )
 ^
cmplx.f:20840:0: warning: 'ilq' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IF( ILQ ) THEN
 ^
cmplx.f:20746:0: warning: 'ilschr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( .NOT.ILSCHR ) THEN
 ^
cmplx.f: In function 'zlals0':
cmplx.f:25696:0: warning: 'difrj' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                            DIFRJ ) / ( POLES( I, 2 )+DJ )
 ^
cmplx.f: In function 'zlahqr':
cmplx.f:24616:0: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                      IF( I2.GT.J )
 ^
cmplx.f: In function 'zlahr2':
cmplx.f:24973:0: warning: 'IMAGPART_EXPR <ei>' may be used uninitialized in this function [-Wmaybe-uninitialized]
       A( K+NB, NB ) = EI
 ^
cmplx.f:24872:0: warning: 'REALPART_EXPR <ei>' may be used uninitialized in this function [-Wmaybe-uninitialized]
       COMPLEX*16        EI
 ^
cmplx.f: In function 'ztrsen':
cmplx.f:49023:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       ELSE IF( LWORK.LT.LWMIN .AND. .NOT.LQUERY ) THEN
 ^
cmplx.f: In function 'zunmql':
cmplx.f:55231:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF( NB.GT.1 .AND. NB.LT.K ) THEN
 ^
cmplx.f: In function 'zungql':
cmplx.f:51959:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
cmplx.f: In function 'zgehrd':
cmplx.f:4925:0: warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized]
          DO 40 I = ILO, IHI - 1 - NX, NB
 ^
cmplx.f: In function 'zgelsd':
cmplx.f:6411:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
cmplx.f: In function 'zgesvd':
cmplx.f:11158:0: warning: 'mnthr' may be used uninitialized in this function [-Wmaybe-uninitialized]
          IF( M.GE.MNTHR ) THEN
 ^
cmplx.f:10741:0: warning: 'wrkbl' may be used uninitialized in this function [-Wmaybe-uninitialized]
      $                   NRVT, WRKBL
 ^
cmplx.f: In function 'zgesvx':
cmplx.f:14642:0: warning: 'smlnum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                ROWCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
cmplx.f:14657:0: warning: 'bignum' may be used uninitialized in this function [-Wmaybe-uninitialized]
                COLCND = MAX( RCMIN, SMLNUM ) / MIN( RCMAX, BIGNUM )
 ^
cmplx.f: In function 'zungrq':
cmplx.f:52750:0: warning: 'nb' may be used uninitialized in this function [-Wmaybe-uninitialized]
             IWS = LDWORK*NB
 ^
gcc -m64 -std=gnu99 -shared -fopenmp -Wl,-z,relro  -o libRlapack.so dlamch.o dlapack.o cmplx.o   -L"../../../lib" -lRblas -lgfortran -lm 
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Lapack.c -o Lapack.o
gcc -m64 -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o lapack.so  Lapack.o  -lR  -L"../../../lib" -lRlapack -L"../../../lib" -lRblas -lgfortran -lm
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
/builddir/build/BUILD/R-3.5.0/lib/libRlapack.so is unchanged
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/modules/X11'
gcc -m64 -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devX11.c -o devX11.o
gcc -m64 -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rotated.c -o rotated.o
gcc -m64 -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbitmap.c -o rbitmap.o
gcc -m64 -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff   -ljpeg -lpng15   -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext   -lX11 -lXt -lXmu  -lR -lm 
gcc -m64 -std=gnu99 -I/usr/include/libpng15     -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dataentry.c -o dataentry.o
gcc -m64 -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro  -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext   -lX11 -lXt -lXmu  -lR -lm 
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/X11'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/X11'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/X11'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/X11'
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library'
mkdir -p -- ../../library
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/profile'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/translations'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/translations'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/translations'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/base'
building package 'base'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/base'
mkdir -p -- ../../../library/base/demo
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/base'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/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
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c text.c -o text.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Rmd5.c -o Rmd5.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c md5.c -o md5.o
md5.c: In function 'md5_finish_ctx':
md5.c:102:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(md5_uint32 *) &ctx->buffer[bytes + pad] = SWAP (ctx->total[0] << 3);
   ^
md5.c:103:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(md5_uint32 *) &ctx->buffer[bytes + pad + 4] = SWAP ((ctx->total[1] << 3) |
   ^
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c signals.c -o signals.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c install.c -o install.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c getfmts.c -o getfmts.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c http.c -o http.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gramLatex.c -o gramLatex.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gramRd.c -o gramRd.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
installing 'sysdata.rda'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/compiler'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/compiler'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/compiler'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/base'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/tools'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/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 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c io.c -o io.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c size.c -o size.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sock.c -o sock.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stubs.c -o stubs.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c utils.c -o utils.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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-3.5.0/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/utils/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/utils/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
installing 'sysdata.rda'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/utils'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/library/grDevices'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/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 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 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c axis_scales.c -o axis_scales.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chull.c -o chull.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devices.c -o devices.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stubs.c -o stubs.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c colors.c -o colors.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devCairo.c -o devCairo.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devPicTeX.c -o devPicTeX.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devPS.c -o devPS.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c devQuartz.c -o devQuartz.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src/cairo'
make[9]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src/cairo'
gcc -m64 -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cairoBM.c -o cairoBM.o
gcc -m64 -std=gnu99 -shared -L"../../../../../lib" -Wl,-z,relro  -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff   -ljpeg -lpng15   -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo   -L"../../../../../lib" -lR -lm 
make[9]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src/cairo'
make[8]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src/cairo'
make[7]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src/cairo'
make[6]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grDevices'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/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 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c base.c -o base.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c graphics.c -o graphics.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c par.c -o par.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plot.c -o plot.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plot3d.c -o plot3d.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stem.c -o stem.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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-3.5.0/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/graphics'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/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 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c kmeans.c -o kmeans.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ansari.c -o ansari.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bandwidths.c -o bandwidths.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chisqsim.c -o chisqsim.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c d2x2xk.c -o d2x2xk.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fexact.c -o fexact.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c kendall.c -o kendall.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ks.c -o ks.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c line.c -o line.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c smooth.c -o smooth.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c prho.c -o prho.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c swilk.c -o swilk.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ksmooth.c -o ksmooth.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c loessc.c -o loessc.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c monoSpl.c -o monoSpl.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c isoreg.c -o isoreg.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Srunmed.c -o Srunmed.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dblcen.c -o dblcen.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c distance.c -o distance.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c hclust-utils.c -o hclust-utils.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c nls.c -o nls.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rWishart.c -o rWishart.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c HoltWinters.c -o HoltWinters.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c PPsum.c -o PPsum.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c arima.c -o arima.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c burg.c -o burg.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c filter.c -o filter.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mAR.c -o mAR.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pacf.c -o pacf.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c starma.c -o starma.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c port.c -o port.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c family.c -o family.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sbart.c -o sbart.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c approx.c -o approx.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c loglin.c -o loglin.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lowess.c -o lowess.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c massdist.c -o massdist.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c splines.c -o splines.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lm.c -o lm.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c complete_cases.c -o complete_cases.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cov.c -o cov.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c deriv.c -o deriv.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fft.c -o fft.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fourier.c -o fourier.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c model.c -o model.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c optim.c -o optim.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c optimize.c -o optimize.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c integrate.c -o integrate.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c random.c -o random.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c distn.c -o distn.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c zeroin.c -o zeroin.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rcont.c -o rcont.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fopenmp -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c influence.c -o influence.o
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c bsplvd.f -o bsplvd.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c bvalue.f -o bvalue.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c bvalus.f -o bvalus.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c loessf.f -o loessf.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
loessf.f:59.14:
            j=DBLE(j)/2.D0                                              
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1893.14:
            m=DBLE(l+u)/2.D0                                            
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1398.20:
                  i=phi(pi(ii))                                         
                    1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:927.12:
         lg=DBLE(lg)/2.D0                                               
            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:522.22:
      if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0                            
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1204.13:
      ifloor=x                                                          
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:834.22:
      if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0                            
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:1582.18:
               i1=dble((d+2)*(d+1))/2.d0                                
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
loessf.f:472.25:
      subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                         1
Warning: Unused dummy argument 'n' at (1)
loessf.f:472.39:
      subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                                       1
Warning: Unused dummy argument 'nc' at (1)
loessf.f:827.31:
      subroutine ehg197(deg,tau,d,f,dk,trl)                             
                               1
Warning: Unused dummy argument 'tau' at (1)
loessf.f:1984.31:
      subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 
                               1
Warning: Unused dummy argument 'kappa' at (1)
loessf.f:1984.47:
      subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 
                                               1
Warning: Unused dummy argument 'nv' at (1)
loessf.f:1984.53:
      subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 
                                                     1
Warning: Unused dummy argument 'nvmax' at (1)
loessf.f:1497.50:
      subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)               
                                                  1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1497.53:
      subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)               
                                                     1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1648.30:
      subroutine lowese(iv,liv,lv,wv,m,z,s)                             
                              1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1648.33:
      subroutine lowese(iv,liv,lv,wv,m,z,s)                             
                                 1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1667.39:
      subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)             
                                       1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1667.42:
      subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)             
                                          1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1699.30:
      subroutine lowesl(iv,liv,lv,wv,m,z,l)                             
                              1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1699.33:
      subroutine lowesl(iv,liv,lv,wv,m,z,l)                             
                                 1
Warning: Unused dummy argument 'lv' at (1)
loessf.f:1721.33:
      subroutine lowesr(yy,iv,liv,lv,wv)                                
                                 1
Warning: Unused dummy argument 'liv' at (1)
loessf.f:1721.36:
      subroutine lowesr(yy,iv,liv,lv,wv)                                
                                    1
Warning: Unused dummy argument 'lv' at (1)
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c ppr.f -o ppr.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c qsbart.f -o qsbart.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c sgram.f -o sgram.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c sinerp.f -o sinerp.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c sslvrg.f -o sslvrg.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c stxwx.f -o stxwx.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c hclust.f -o hclust.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c kmns.f -o kmns.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c eureka.f -o eureka.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c stl.f -o stl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64 -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules -c portsrc.f -o portsrc.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
portsrc.f: In function 'i7do':
portsrc.f:6448:0: warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
          JPU = JPNTR(JCOL+1) - 1
 ^
portsrc.f: In function 'df7dhb':
portsrc.f:12276:0: warning: 'pp1o2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       HPI = HES + PP1O2
 ^
portsrc.f: In function 'dl7mst':
portsrc.f:5328:0: warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
 ^
portsrc.f:5463:0: warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
               IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
 ^
portsrc.f: In function 'dg7qts':
portsrc.f:10090:0: warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
 ^
portsrc.f:10008:0: warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
 ^
portsrc.f:10003:0: warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
       LK = DMAX1(LK, PHI*W(PHIPIN))
 ^
portsrc.f:10144:0: warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (KA .GE. KAMIN) GO TO 340
 ^
portsrc.f: In function 'dd7dgb':
portsrc.f:11900:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:11903:0: warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(DST0) = DNWTST
 ^
portsrc.f: In function 'dg7qsb':
portsrc.f:2390:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:2389:0: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  60   V(DST0) = DS0
 ^
portsrc.f: In function 'dl7msb':
portsrc.f:7892:0: warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
       V(NREDUC) = NRED
 ^
portsrc.f:7891:0: warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  90   V(DST0) = DS0
 ^
portsrc.f: In function 'df7hes':
portsrc.f:8370:0: warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
  210  IV(FDH) = HES
 ^
portsrc.f: In function 'dparck':
portsrc.f:3456:0: warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       IF (LIV .LT. MIV2) GO TO 300
 ^
portsrc.f: In function 'drn2gb':
portsrc.f:11737:0: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  270  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 ^
portsrc.f:11694:0: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
portsrc.f:11694:0: warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f: In function 'drn2g':
portsrc.f:440:0: warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  300  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 ^
portsrc.f:348:0: warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
portsrc.f:348:0: warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -m64  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c lminfl.f -o lminfl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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 -L../../../../lib -lRlapack -L../../../../lib -lRblas -lgfortran -lm -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/stats/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/stats/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/stats'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/datasets'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/datasets'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/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 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c do_substitute_direct.c -o do_substitute_direct.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c methods_list_dispatch.c -o methods_list_dispatch.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c slot.c -o slot.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c class_support.c -o class_support.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c tests.c -o tests.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c utils.c -o utils.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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-3.5.0/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/methods/src'
make[5]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/methods/src'
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/methods'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[4]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/grid'
make[4]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grid'
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grid/src'
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 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 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gpar.c -o gpar.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c grid.c -o grid.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c just.c -o just.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c layout.c -o layout.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c matrix.c -o matrix.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c register.c -o register.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c state.c -o state.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c unit.c -o unit.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c util.c -o util.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c viewport.c -o viewport.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/grid/src'
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making splines.d from splines.c
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c splines.c -o splines.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/splines/src'
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building package 'tcltk'
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making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -m64 -std=gnu99 -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 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -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 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c tcltk.c -o tcltk.o
gcc -m64 -std=gnu99 -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 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c tcltk_unix.c -o tcltk_unix.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11 -lm -L../../../../lib -lR
make[5]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/tcltk/src'
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building package 'parallel'
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making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rngstream.c -o rngstream.o
gcc -m64 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fork.c -o fork.o
gcc -m64 -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[6]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/parallel/src'
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building all R object docs
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    serialize                               html  
    setTimeLimit                            html  
    sets                                    html  
    shQuote                                 html  
    showConnections                         html  
    sign                                    html  
    sink                                    html  
    slice.index                             html  
    slotOp                                  html  
    socketSelect                            html  
    solve                                   html  
    sort                                    html  
    source                                  html  
    split                                   html  
    sprintf                                 html  
    srcfile                                 html  
    standardGeneric                         html  
    startsWith                              html  
    stop                                    html  
    stopifnot                               html  
    strptime                                html  
    strrep                                  html  
    strsplit                                html  
    strtoi                                  html  
    strtrim                                 html  
    structure                               html  
    strwrap                                 html  
    subset                                  html  
    substitute                              html  
    substr                                  html  
    sum                                     html  
    summary                                 html  
    svd                                     html  
    sweep                                   html  
    switch                                  html  
    sys.parent                              html  
    sys.source                              html  
    system                                  html  
    system.file                             html  
    system.time                             html  
    system2                                 html  
    t                                       html  
    table                                   html  
    tabulate                                html  
    tapply                                  html  
    taskCallback                            html  
    taskCallbackManager                     html  
    taskCallbackNames                       html  
    tempfile                                html  
    textconnections                         html  
    tilde                                   html  
    timezones                               html  
    toString                                html  
    trace                                   html  
    traceback                               html  
    tracemem                                html  
    transform                               html  
    trimws                                  html  
    try                                     html  
    typeof                                  html  
    unique                                  html  
    unlink                                  html  
    unlist                                  html  
    unname                                  html  
    userhooks                               html  
    utf8Conversion                          html  
    validUTF8                               html  
    vector                                  html  
    warning                                 html  
    warnings                                html  
    weekday.POSIXt                          html  
    which                                   html  
    which.min                               html  
    with                                    html  
    withVisible                             html  
    write                                   html  
    writeLines                              html  
    xtfrm                                   html  
    zMachine                                html  
    zScript                                 html  
    zapsmall                                html  
    zpackages                               html  
    zutils                                  html  
    Signals                                 html  
  converting help for package 'tools'
    CRANtools                               html  
    HTMLheader                              html  
    HTMLlinks                               html  
    QC                                      html  
    Rcmd                                    html  
    Rd2HTML                                 html  
    Rd2txt_options                          html  
    RdTextFilter                            html  
    Rdiff                                   html  
    Rdindex                                 html  
    Rdutils                                 html  
    SweaveTeXFilter                         html  
    add_datalist                            html  
    assertCondition                         html  
    bibstyle                                html  
    buildVignette                           html  
    buildVignettes                          html  
    charsets                                html  
    checkFF                                 html  
    checkMD5sums                            html  
    checkPoFiles                            html  
    checkRd                                 html  
    checkRdaFiles                           html  
    checkTnF                                html  
    checkVignettes                          html  
    check_packages_in_dir                   html  
Rd warning: /builddir/build/BUILD/R-3.5.0/src/library/tools/man/check_packages_in_dir.Rd:121: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    codoc                                   html  
    compactPDF                              html  
    delimMatch                              html  
    dependsOnPkgs                           html  
    encoded                                 html  
    fileutils                               html  
    find_gs_cmd                             html  
    getVignetteInfo                         html  
    loadRdMacros                            html  
    makeLazyLoading                         html  
    make_translations_pkg                   html  
    makevars                                html  
    md5sum                                  html  
    package_dependencies                    html  
    package_native_routine_registration_skeleton
                                            html  
    parseLatex                              html  
    parse_Rd                                html  
    print.via.format                        html  
    pskill                                  html  
    psnice                                  html  
    read.00Index                            html  
    showNonASCII                            html  
    startDynamicHelp                        html  
    testInstalledPackage                    html  
    texi2dvi                                html  
    toHTML                                  html  
    toRd                                    html  
    toTitleCase                             html  
    tools-defunct                           html  
    tools-deprecated                        html  
    tools-package                           html  
    undoc                                   html  
    update_pkg_po                           html  
    vignetteDepends                         html  
    vignetteEngine                          html  
    writePACKAGES                           html  
    xgettext                                html  
  converting help for package 'utils'
    BATCH                                   html  
    INSTALL                                 html  
    PkgUtils                                html  
    Question                                html  
    REMOVE                                  html  
    RHOME                                   html  
    RShowDoc                                html  
    RSiteSearch                             html  
    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  
    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  
    chooseBioCmirror                        html  
    chooseCRANmirror                        html  
    citEntry                                html  
    citation                                html  
    cite                                    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  
    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  
    menu                                    html  
    methods                                 html  
    mirrorAdmin                             html  
    modifyList                              html  
    news                                    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  
    recover                                 html  
    relist                                  html  
    remove.packages                         html  
    removeSource                            html  
    roman                                   html  
    rtags                                   html  
    savehistory                             html  
    select.list                             html  
    sessionInfo                             html  
    setRepositories                         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  
    write.table                             html  
    zip                                     html  
    COMPILE                                 html  
    LINK                                    html  
    memory.size                             html  
    nsl                                     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  
    cairo                                   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  
    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  
    recordGraphics                          html  
    recordplot                              html  
    rgb                                     html  
    rgb2hsv                                 html  
    trans3d                                 html  
    xfig                                    html  
    xy.coords                               html  
    xyTable                                 html  
    xyz.coords                              html  
    png                                     html  
    quartz                                  html  
    quartzFonts                             html  
    savePlot                                html  
    x11                                     html  
    x11Fonts                                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                                    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  
    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  
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    Methods_for_Nongenerics                 html  
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    ObjectsWithPackage-class                html  
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    methods-package                         html  
    new                                     html  
    nonStructure-class                      html  
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    signature-class                         html  
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    stdRefClass                             html  
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    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  
    drawDetails                             html  
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    explode                                 html  
    gEdit                                   html  
    gPath                                   html  
    getNames                                html  
    gpar                                    html  
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    grid.display.list                       html  
    grid.draw                               html  
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    grid.null                               html  
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    grid.path                               html  
    grid.place                              html  
    grid.plot.and.legend                    html  
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    grid.polygon                            html  
    grid.pretty                             html  
    grid.raster                             html  
    grid.record                             html  
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    grid.segments                           html  
    grid.set                                html  
    grid.show.layout                        html  
    grid.show.viewport                      html  
    grid.text                               html  
    grid.xaxis                              html  
    grid.xspline                            html  
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    grobName                                html  
    grobWidth                               html  
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    legendGrob                              html  
    makeContent                             html  
    plotViewport                            html  
    resolveRasterSize                       html  
    showGrob                                html  
    showViewport                            html  
    stringWidth                             html  
    unit                                    html  
    unit.c                                  html  
    unit.length                             html  
    unit.pmin                               html  
    unit.rep                                html  
    valid.just                              html  
    validDetails                            html  
    viewport                                html  
    viewports                               html  
    vpPath                                  html  
    widthDetails                            html  
    xDetails                                html  
    xsplinePoints                           html  
  converting help for package 'splines'
    asVector                                html  
    backSpline                              html  
    bs                                      html  
    interpSpline                            html  
    ns                                      html  
    periodicSpline                          html  
    polySpline                              html  
    predict.bSpline                         html  
    predict.bs                              html  
    splineDesign                            html  
    splineKnots                             html  
    splineOrder                             html  
    splines-package                         html  
    xyVector                                html  
  converting help for package 'stats4'
    coef-methods                            html  
    confint-methods                         html  
    logLik-methods                          html  
    mle-class                               html  
    mle                                     html  
    plot-methods                            html  
    profile-methods                         html  
    profile.mle-class                       html  
    show-methods                            html  
    stats4-package                          html  
    summary-methods                         html  
    summary.mle-class                       html  
    update-methods                          html  
    vcov-methods                            html  
  converting help for package 'tcltk'
    TclInterface                            html  
    TkCommands                              html  
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    TkWidgets                               html  
    tclServiceMode                          html  
    tcltk-defunct                           html  
    tcltk-package                           html  
    tkProgressBar                           html  
    tkStartGUI                              html  
    tk_choose.dir                           html  
    tk_choose.files                         html  
    tk_messageBox                           html  
    tk_select.list                          html  
    tkpager                                 html  
  converting help for package 'compiler'
    compile                                 html  
  converting help for package 'parallel'
    RngStream                               html  
    clusterApply                            html  
    detectCores                             html  
    makeCluster                             html  
    parallel-package                        html  
    splitIndices                            html  
    children                                html  
    mcaffinity                              html  
    mcfork                                  html  
    mclapply                                html  
    mcparallel                              html  
    pvec                                    html  
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/Recommended'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/tmp/RtmpTtIfxi/R.INSTALL73dd6e29d346/MASS/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c MASS.c -o MASS.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lqs.c -o lqs.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o MASS.so MASS.o lqs.o -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpTtIfxi/R.INSTALL73dd6e29d346/MASS/src'
installing to /builddir/build/BUILD/R-3.5.0/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'
    finding HTML links ... done
    Aids2                                   html  
    Animals                                 html  
    Boston                                  html  
    Cars93                                  html  
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    DDT                                     html  
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    MASS-internal                           html  
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    Null                                    html  
    OME                                     html  
    Pima.tr                                 html  
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    SP500                                   html  
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    Sitka89                                 html  
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    UScrime                                 html  
    VA                                      html  
    abbey                                   html  
    accdeaths                               html  
    addterm                                 html  
    anorexia                                html  
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    bacteria                                html  
    bandwidth.nrd                           html  
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    con2tr                                  html  
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    corresp                                 html  
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    fgl                                     html  
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    forbes                                  html  
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    galaxies                                html  
    gamma.dispersion                        html  
    gamma.shape.glm                         html  
    gehan                                   html  
    genotype                                html  
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    gilgais                                 html  
    ginv                                    html  
    glm.convert                             html  
    glm.nb                                  html  
    glmmPQL                                 html  
    hills                                   html  
    hist.scott                              html  
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    leuk                                    html  
    lm.gls                                  html  
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    loglm1                                  html  
    logtrans                                html  
    lqs                                     html  
    mammals                                 html  
    mca                                     html  
    mcycle                                  html  
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    motors                                  html  
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    mvrnorm                                 html  
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    pairs.lda                               html  
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    phones                                  html  
    plot.lda                                html  
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    polr                                    html  
    predict.glmmPQL                         html  
    predict.lda                             html  
    predict.lqs                             html  
    predict.mca                             html  
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    qda                                     html  
    quine                                   html  
    rational                                html  
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    rlm                                     html  
    rms.curv                                html  
    rnegbin                                 html  
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    sammon                                  html  
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    topo                                    html  
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    whiteside                               html  
    width.SJ                                html  
    write.matrix                            html  
    wtloss                                  html  
** 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
** libs
make[3]: Entering directory `/tmp/RtmpYi467F/R.INSTALL744928850d05/lattice/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c threeDplot.c -o threeDplot.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o lattice.so init.o threeDplot.o -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpYi467F/R.INSTALL744928850d05/lattice/src'
installing to /builddir/build/BUILD/R-3.5.0/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
    Lattice                                 html  
    Rows                                    html  
    USMortality                             html  
    axis.default                            html  
    banking                                 html  
    barchart.table                          html  
    barley                                  html  
    cloud                                   html  
    draw.colorkey                           html  
    draw.key                                html  
    environmental                           html  
    ethanol                                 html  
    histogram                               html  
    interaction                             html  
    lattice.options                         html  
    latticeParseFormula                     html  
    level.colors                            html  
    levelplot                               html  
    llines                                  html  
    lset                                    html  
    make.groups                             html  
    melanoma                                html  
    oneway                                  html  
    packet.panel.default                    html  
    panel.axis                              html  
    panel.barchart                          html  
    panel.bwplot                            html  
    panel.cloud                             html  
    panel.densityplot                       html  
    panel.dotplot                           html  
    panel.functions                         html  
    panel.histogram                         html  
    panel.levelplot                         html  
    panel.loess                             html  
    panel.number                            html  
    panel.pairs                             html  
    panel.parallel                          html  
    panel.qqmath                            html  
    panel.qqmathline                        html  
    panel.smoothScatter                     html  
    panel.spline                            html  
    panel.stripplot                         html  
    panel.superpose                         html  
    panel.violin                            html  
    panel.xyplot                            html  
    prepanel.default                        html  
    prepanel.functions                      html  
    print.trellis                           html  
    qq                                      html  
    qqmath                                  html  
    rfs                                     html  
    shingles                                html  
    simpleKey                               html  
    simpleTheme                             html  
    singer                                  html  
    splom                                   html  
    strip.default                           html  
    tmd                                     html  
    trellis.device                          html  
    trellis.object                          html  
    trellis.par.get                         html  
    update.trellis                          html  
    utilities.3d                            html  
    xyplot                                  html  
    xyplot.ts                               html  
** 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
** libs
make[3]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c CHMfactor.c -o CHMfactor.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Csparse.c -o Csparse.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c TMatrix_as.c -o TMatrix_as.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Tsparse.c -o Tsparse.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Mutils.c -o Mutils.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chm_common.c -o chm_common.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
     csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
                  ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cs_utils.c -o cs_utils.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dense.c -o dense.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgCMatrix.c -o dgCMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgTMatrix.c -o dgTMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgeMatrix.c -o dgeMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dpoMatrix.c -o dpoMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dppMatrix.c -o dppMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dsCMatrix.c -o dsCMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dsyMatrix.c -o dsyMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dspMatrix.c -o dspMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dtCMatrix.c -o dtCMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dtTMatrix.c -o dtTMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dtrMatrix.c -o dtrMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dtpMatrix.c -o dtpMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c factorizations.c -o factorizations.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ldense.c -o ldense.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgCMatrix.c -o lgCMatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sparseQR.c -o sparseQR.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c abIndex.c -o abIndex.o
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[5]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD/Lib'
make[5]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD'
( cd Source ; make clean )
make[5]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD/Source'
make[5]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD'
( cd Source ; make clean )
make[5]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD/Source'
make[5]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD/Source'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/SuiteSparse_config'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/SuiteSparse_config'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD'
( cd Lib ; make -f "/builddir/build/BUILD/R-3.5.0/etc/Makeconf" -f Makefile )
make[5]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD/Lib'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
../Check/cholmod_check.c: In function 'check_factor.constprop.3':
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
../Check/cholmod_check.c: In function 'check_factor.constprop.3':
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
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/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/CHOLMOD'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD'
( cd Source ; make -f "/builddir/build/BUILD/R-3.5.0/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD/Source'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c colamd_global.c -o colamd_global.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c colamd.c -o colamd.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/COLAMD'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD'
( cd Source ; make -f "/builddir/build/BUILD/R-3.5.0/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD/Source'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -I../Include -DDLONG -c amd_global.c -o amd_l_global.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 amd_i_global.o amd_l_global.o 
make[5]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD/Source'
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/AMD'
make[4]: Entering directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/SuiteSparse_config'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG -DNTIMER  -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src/SuiteSparse_config'
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -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 -L/builddir/build/BUILD/R-3.5.0/lib -lRlapack -L/builddir/build/BUILD/R-3.5.0/lib -lRblas -lgfortran -lm -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/src'
installing to /builddir/build/BUILD/R-3.5.0/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  
Rd warning: /tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/man/abIndex-class.Rd:80: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
    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  
    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  
Rd warning: /tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/man/image-methods.Rd:53: file link 'panel.levelplot.raster' in package 'lattice' does not exist and so has been treated as a topic
    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  
    matrix-products                         html  
Rd warning: /tmp/Rtmpu4n4R7/R.INSTALL747467382145/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic
    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  
** building package indices
Loading required package: Matrix
** 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
** libs
make[3]: Entering directory `/tmp/RtmpuChzlz/R.INSTALL78d66b7da6f3/nlme/src'
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c chol.f -o chol.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c corStruct.c -o corStruct.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gnls.c -o gnls.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c matrix.c -o matrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c nlOptimizer.c -o nlOptimizer.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c nlme.c -o nlme.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c nlmefit.c -o nlmefit.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pdMat.c -o pdMat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fvisibility=hidden -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pythag.c -o pythag.o
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c rs.f -o rs.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -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 -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpuChzlz/R.INSTALL78d66b7da6f3/nlme/src'
installing to /builddir/build/BUILD/R-3.5.0/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
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    ACF.gls                                 html  
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    intervals.gls                           html  
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    isBalanced                              html  
    isInitialized                           html  
    lmList                                  html  
    lmList.groupedData                      html  
    lme                                     html  
    lme.groupedData                         html  
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    logDet                                  html  
    logDet.corStruct                        html  
    logDet.pdMat                            html  
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    logLik.lmList                           html  
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    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  
    pdBlocked                               html  
    pdClasses                               html  
    pdCompSymm                              html  
    pdConstruct                             html  
    pdConstruct.pdBlocked                   html  
    pdDiag                                  html  
    pdFactor                                html  
    pdFactor.reStruct                       html  
    pdIdent                                 html  
    pdLogChol                               html  
    pdMat                                   html  
    pdMatrix                                html  
    pdMatrix.reStruct                       html  
    pdNatural                               html  
    pdSymm                                  html  
    phenoModel                              html  
    plot.ACF                                html  
    plot.Variogram                          html  
    plot.augPred                            html  
    plot.compareFits                        html  
    plot.gls                                html  
    plot.intervals.lmList                   html  
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    plot.nffGroupedData                     html  
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    predict.nlme                            html  
    print.summary.pdMat                     html  
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    qqnorm.gls                              html  
    qqnorm.lme                              html  
    quinModel                               html  
    random.effects                          html  
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    recalc.corStruct                        html  
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    solve.pdMat                             html  
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    summary.varFunc                         html  
    update.modelStruct                      html  
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    varClasses                              html  
    varComb                                 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
** libs
make[3]: Entering directory `/tmp/RtmpT0JAFt/R.INSTALL790d7df7be38/survival/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agexact.c -o agexact.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agfit4.c -o agfit4.o
agfit4.c: In function 'agfit4':
agfit4.c:329:20: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 if (tstop[p] < dtime) break; /* no more to add */
                    ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agfit5.c -o agfit5.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agmart.c -o agmart.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agmart2.c -o agmart2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agmart3.c -o agmart3.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agscore.c -o agscore.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agsurv3.c -o agsurv3.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agsurv4.c -o agsurv4.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c agsurv5.c -o agsurv5.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chinv2.c -o chinv2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chinv3.c -o chinv3.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cholesky2.c -o cholesky2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cholesky3.c -o cholesky3.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chsolve2.c -o chsolve2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chsolve3.c -o chsolve3.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c concordance1.c -o concordance1.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cox_Rcallback.c -o cox_Rcallback.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxcount1.c -o coxcount1.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxdetail.c -o coxdetail.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxexact.c -o coxexact.o
coxexact.c: In function 'coxexact':
coxexact.c:309:27: warning: 'sstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 d0 = coxd0(ndeath, nrisk, score+sstart, dmem0, maxdeath);
                           ^
coxexact.c:151:17: warning: 'nrisk' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (maxdeath*nrisk > temp) temp = maxdeath*nrisk;
                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxfit5.c -o coxfit5.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxfit6.c -o coxfit6.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxmart.c -o coxmart.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxmart2.c -o coxmart2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxph_wtest.c -o coxph_wtest.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxsafe.c -o coxsafe.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxscho.c -o coxscho.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxscore.c -o coxscore.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dmatrix.c -o dmatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c doloop.c -o doloop.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c finegray.c -o finegray.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pyears1.c -o pyears1.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pyears2.c -o pyears2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pyears3b.c -o pyears3b.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pystep.c -o pystep.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survConcordance.c -o survConcordance.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survdiff2.c -o survdiff2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survfit4.c -o survfit4.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survfitci.c -o survfitci.o
survfitci.c: In function 'survfitci':
survfitci.c:18:14: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double **umat;     /* per subject leverage at this time point */
              ^
survfitci.c:46:38: warning: 'usave' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double **pmat, **vmat, *cumhaz, *usave;
                                      ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survpenal.c -o survpenal.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survreg6.c -o survreg6.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survreg7.c -o survreg7.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survregc1.c -o survregc1.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survregc2.c -o survregc2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c survsplit.c -o survsplit.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c tmerge.c -o tmerge.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.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 coxscore.o dmatrix.o doloop.o finegray.o init.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpT0JAFt/R.INSTALL790d7df7be38/survival/src'
installing to /builddir/build/BUILD/R-3.5.0/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  
    aareg                                   html  
    aeqSurv                                 html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    cch                                     html  
    cgd                                     html  
    cgd0                                    html  
    cipoisson                               html  
Rd warning: /tmp/RtmpT0JAFt/R.INSTALL790d7df7be38/survival/man/cipoisson.Rd:59: file link 'ppois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpT0JAFt/R.INSTALL790d7df7be38/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic
    clogit                                  html  
    cluster                                 html  
    colon                                   html  
    cox.zph                                 html  
    coxph                                   html  
    coxph.control                           html  
    coxph.detail                            html  
    coxph.object                            html  
    coxph.wtest                             html  
    dsurvreg                                html  
    finegray                                html  
    flchain                                 html  
    frailty                                 html  
    genfan                                  html  
    heart                                   html  
    is.ratetable                            html  
    kidney                                  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  
    neardate                                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  
    pspline                                 html  
    pyears                                  html  
    quantile.survfit                        html  
    ratetable                               html  
    ratetableDate                           html  
    rats                                    html  
    rats2                                   html  
    residuals.coxph                         html  
    residuals.survreg                       html  
    retinopathy                             html  
    rhDNase                                 html  
    ridge                                   html  
    stanford2                               html  
    statefig                                html  
    strata                                  html  
    summary.aareg                           html  
    summary.coxph                           html  
    summary.pyears                          html  
    summary.survexp                         html  
    summary.survfit                         html  
    survConcordance                         html  
    survSplit                               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  
    survfitcoxph.fit                        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  
    untangle.specials                       html  
    uspop2                                  html  
    veteran                                 html  
** 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
** 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
** libs
make[3]: Entering directory `/tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c clara.c -o clara.o
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c daisy.f -o daisy.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dysta.f -o dysta.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fanny.c -o fanny.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mona.c -o mona.o
mona.c: In function 'clmona_':
mona.c:261:10: warning: 'nelbb' may be used uninitialized in this function [-Wmaybe-uninitialized]
   ner[k] = nelbb;
          ^
mona.c:248:7: warning: 'lcc' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lcc, nelbb;
       ^
mona.c:235:6: warning: 'jtelz' may be used uninitialized in this function [-Wmaybe-uninitialized]
      km = ka + jtel2;
      ^
mona.c:218:24: warning: 'jtel' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if(verbose) Rprintf("  for(j ..) -> jma=%d, jtel(.,z) = (%d, %d)", jma, jtel, jtelz);
                        ^
mona.c:274:11: warning: 'jma' may be used uninitialized in this function [-Wmaybe-uninitialized]
  lava[km] = jma;
           ^
mona.c:211:8: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
   jtel = c + d;
        ^
mona.c:211:8: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized]
mona.c:212:9: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized]
   jtelz = a + b;
         ^
mona.c:212:9: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pam.c -o pam.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sildist.c -o sildist.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c spannel.c -o spannel.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c twins.c -o twins.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -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 -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/src'
installing to /builddir/build/BUILD/R-3.5.0/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  
Rd warning: /tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
    clusplot.partition                      html  
    cluster-internal                        html  
    coef.hclust                             html  
    daisy                                   html  
    diana                                   html  
    dissimilarity.object                    html  
    ellipsoidhull                           html  
Rd warning: /tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/man/ellipsoidhull.Rd:36: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
    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  
Rd warning: /tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic
    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  
Rd warning: /tmp/RtmpwguMG1/R.INSTALL7a3163c769a9/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic
    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
** 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
** libs
make[3]: Entering directory `/tmp/RtmpnySI8W/R.INSTALL7ae6245128ea/foreign/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c R_systat.c -o R_systat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Rdbfread.c -o Rdbfread.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c Rdbfwrite.c -o Rdbfwrite.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c SASxport.c -o SASxport.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c avl.c -o avl.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbfopen.c -o dbfopen.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c file-handle.c -o file-handle.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c format.c -o format.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c minitab.c -o minitab.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pfm-read.c -o pfm-read.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sfm-read.c -o sfm-read.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c spss.c -o spss.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stataread.c -o stataread.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -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-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpnySI8W/R.INSTALL7ae6245128ea/foreign/src'
installing to /builddir/build/BUILD/R-3.5.0/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
** libs
make[3]: Entering directory `/tmp/RtmpTJ6W3d/R.INSTALL7b262b97ed67/KernSmooth/src'
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c blkest.f -o blkest.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c cp.f -o cp.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dgedi.f -o dgedi.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dgefa.f -o dgefa.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c dgesl.f -o dgesl.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c linbin.f -o linbin.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c linbin2D.f -o linbin2D.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c locpoly.f -o locpoly.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c rlbin.f -o rlbin.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c sdiag.f -o sdiag.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gfortran -m64   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7 -I/usr/lib64/gfortran/modules  -c sstdiag.f -o sstdiag.o
Warning: Nonexistent include directory "/usr/lib64/gfortran/modules"
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -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 -L/builddir/build/BUILD/R-3.5.0/lib -lRblas -lgfortran -lm -lgfortran -lm -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpTJ6W3d/R.INSTALL7b262b97ed67/KernSmooth/src'
installing to /builddir/build/BUILD/R-3.5.0/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
** libs
make[3]: Entering directory `/tmp/RtmpvTbjY8/R.INSTALL7b60447048c4/rpart/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c anova.c -o anova.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c anovapred.c -o anovapred.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c branch.c -o branch.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bsplit.c -o bsplit.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c choose_surg.c -o choose_surg.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fix_cp.c -o fix_cp.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c free_tree.c -o free_tree.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gini.c -o gini.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c graycode.c -o graycode.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c insert_split.c -o insert_split.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c make_cp_list.c -o make_cp_list.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c make_cp_table.c -o make_cp_table.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mysort.c -o mysort.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c nodesplit.c -o nodesplit.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c partition.c -o partition.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c poisson.c -o poisson.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pred_rpart.c -o pred_rpart.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c print_tree.c -o print_tree.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpart.c -o rpart.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpart_callback.c -o rpart_callback.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpartexp.c -o rpartexp.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpartexp2.c -o rpartexp2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpcountup.c -o rpcountup.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpmatrix.c -o rpmatrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rundown.c -o rundown.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rundown2.c -o rundown2.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c surrogate.c -o surrogate.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c usersplit.c -o usersplit.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c xpred.c -o xpred.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c xval.c -o xval.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -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-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpvTbjY8/R.INSTALL7b60447048c4/rpart/src'
installing to /builddir/build/BUILD/R-3.5.0/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                                  html  
    stagec                                  html  
    summary.rpart                           html  
    text.rpart                              html  
    xpred.rpart                             html  
** 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
** libs
make[3]: Entering directory `/tmp/RtmpI6ddxw/R.INSTALL7bd32e868557/class/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c class.c -o class.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o class.so class.o -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpI6ddxw/R.INSTALL7bd32e868557/class/src'
installing to /builddir/build/BUILD/R-3.5.0/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
** libs
make[3]: Entering directory `/tmp/RtmpzL3cWV/R.INSTALL7bee2718b0c4/nnet/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c nnet.c -o nnet.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o nnet.so nnet.o -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpzL3cWV/R.INSTALL7bee2718b0c4/nnet/src'
installing to /builddir/build/BUILD/R-3.5.0/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
** libs
make[3]: Entering directory `/tmp/Rtmp2dWQwy/R.INSTALL7c1678378dc5/spatial/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c krc.c -o krc.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pps.c -o pps.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o spatial.so init.o krc.o pps.o -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/Rtmp2dWQwy/R.INSTALL7c1678378dc5/spatial/src'
installing to /builddir/build/BUILD/R-3.5.0/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
** libs
make[3]: Entering directory `/tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/src'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c coxph.c -o coxph.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c discrete.c -o discrete.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gdi.c -o gdi.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c magic.c -o magic.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mat.c -o mat.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c matrix.c -o matrix.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mgcv.c -o mgcv.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c misc.c -o misc.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mvn.c -o mvn.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qp.c -o qp.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c soap.c -o soap.o
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sparse-smooth.c -o sparse-smooth.o
sparse-smooth.c: In function 'Rkradius':
sparse-smooth.c:768:17: warning: unused variable 'dis' [-Wunused-variable]
   double *X,*x,*dis,*r,*xx,*ddat;
                 ^
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c tprs.c -o tprs.o
gcc -m64 -std=gnu99 -shared -L/builddir/build/BUILD/R-3.5.0/lib -Wl,-z,relro -o mgcv.so coxph.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 tprs.o -L/builddir/build/BUILD/R-3.5.0/lib -lRlapack -L/builddir/build/BUILD/R-3.5.0/lib -lRblas -lgfortran -lm -fopenmp -L/builddir/build/BUILD/R-3.5.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/src'
installing to /builddir/build/BUILD/R-3.5.0/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  
    Predict.matrix                          html  
    Predict.matrix.cr.smooth                html  
    Predict.matrix.soap.film                html  
    Rrank                                   html  
    Sl.initial.repara                       html  
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    Sl.setup                                html  
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    bam                                     html  
Rd warning: /tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/man/bam.Rd:14: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/man/bam.Rd:129: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/man/bam.Rd:188: file link 'makeForkCluster' in package 'parallel' does not exist and so has been treated as a topic
    bam.update                              html  
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    mgcv-parallel                           html  
Rd warning: /tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/man/mgcv-parallel.Rd:11: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
    mini.roots                              html  
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Rd warning: /tmp/RtmpWxTxHh/R.INSTALL7c3547e8ffdb/mgcv/man/predict.bam.Rd:76: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    predict.gam                             html  
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    rTweedie                                html  
    random.effects                          html  
    residuals.gam                           html  
    rig                                     html  
    rmvn                                    html  
    s                                       html  
    scat                                    html  
    sdiag                                   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.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  
    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-3.5.0/src/library/Recommended'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library/Recommended'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library'
building/updating vignettes for package 'grid' ...
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0'
configuring Java ...
Java interpreter : /usr/bin/java
Java version     : 1.8.0_171
Java home path   : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-7.b10.el7.ppc64/jre
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/ppc64/server -ljvm
make[2]: Entering directory `/tmp/Rjavareconf.WCZzIq'
gcc -m64 -std=gnu99 -I"/builddir/build/BUILD/R-3.5.0/include" -DNDEBUG   -I/usr/local/include   -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
 #include <jni.h>
                 ^
compilation terminated.
make[2]: *** [conftest.o] Error 1
make[2]: Leaving directory `/tmp/Rjavareconf.WCZzIq'
Unable to compile a JNI program
JAVA_HOME        : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-7.b10.el7.ppc64/jre
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /builddir/build/BUILD/R-3.5.0
Done.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0'
+ cd src/nmath/standalone
+ make
(cd ../../include; make Rmath.h)
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/include'
make[1]: `Rmath.h' is up to date.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/include'
Copying source files
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/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-3.5.0/src/nmath/standalone'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/nmath/standalone'
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mlutils.c -o mlutils.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c d1mach.c -o d1mach.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c i1mach.c -o i1mach.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fmax2.c -o fmax2.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fmin2.c -o fmin2.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fprec.c -o fprec.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fround.c -o fround.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ftrunc.c -o ftrunc.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sign.c -o sign.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fsign.c -o fsign.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c imax2.c -o imax2.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c imin2.c -o imin2.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chebyshev.c -o chebyshev.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c log1p.c -o log1p.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgammacor.c -o lgammacor.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gammalims.c -o gammalims.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stirlerr.c -o stirlerr.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bd0.c -o bd0.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gamma.c -o gamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgamma.c -o lgamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gamma_cody.c -o gamma_cody.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c beta.c -o beta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lbeta.c -o lbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c polygamma.c -o polygamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cospi.c -o cospi.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_i.c -o bessel_i.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_j.c -o bessel_j.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_k.c -o bessel_k.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_y.c -o bessel_y.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c choose.c -o choose.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c snorm.c -o snorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sexp.c -o sexp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgamma.c -o dgamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pgamma.c -o pgamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qgamma.c -o qgamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rgamma.c -o rgamma.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbeta.c -o dbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pbeta.c -o pbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qbeta.c -o qbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbeta.c -o rbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dunif.c -o dunif.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c punif.c -o punif.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qunif.c -o qunif.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c runif.c -o runif.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnorm.c -o dnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnorm.c -o pnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnorm.c -o qnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnorm.c -o rnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dlnorm.c -o dlnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plnorm.c -o plnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qlnorm.c -o qlnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlnorm.c -o rlnorm.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c df.c -o df.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pf.c -o pf.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qf.c -o qf.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rf.c -o rf.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnf.c -o dnf.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dt.c -o dt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pt.c -o pt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qt.c -o qt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rt.c -o rt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnt.c -o dnt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dchisq.c -o dchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pchisq.c -o pchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qchisq.c -o qchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rchisq.c -o rchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnchisq.c -o rnchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbinom.c -o dbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pbinom.c -o pbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qbinom.c -o qbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbinom.c -o rbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rmultinom.c -o rmultinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dcauchy.c -o dcauchy.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pcauchy.c -o pcauchy.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qcauchy.c -o qcauchy.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rcauchy.c -o rcauchy.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dexp.c -o dexp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pexp.c -o pexp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qexp.c -o qexp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rexp.c -o rexp.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgeom.c -o dgeom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pgeom.c -o pgeom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qgeom.c -o qgeom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rgeom.c -o rgeom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dhyper.c -o dhyper.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c phyper.c -o phyper.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qhyper.c -o qhyper.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rhyper.c -o rhyper.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnbinom.c -o dnbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnbinom.c -o pnbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnbinom.c -o qnbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnbinom.c -o rnbinom.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dpois.c -o dpois.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ppois.c -o ppois.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qpois.c -o qpois.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpois.c -o rpois.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dweibull.c -o dweibull.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pweibull.c -o pweibull.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qweibull.c -o qweibull.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rweibull.c -o rweibull.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dlogis.c -o dlogis.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plogis.c -o plogis.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qlogis.c -o qlogis.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlogis.c -o rlogis.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnchisq.c -o dnchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnchisq.c -o pnchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnchisq.c -o qnchisq.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnbeta.c -o dnbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnbeta.c -o pnbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnbeta.c -o qnbeta.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnf.c -o pnf.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnt.c -o pnt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnf.c -o qnf.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnt.c -o qnt.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ptukey.c -o ptukey.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qtukey.c -o qtukey.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c toms708.c -o toms708.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c wilcox.c -o wilcox.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c signrank.c -o signrank.o
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -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-3.5.0/src/nmath/standalone'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/nmath/standalone'
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c mlutils.c -o mlutils.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c d1mach.c -o d1mach.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c i1mach.c -o i1mach.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fmax2.c -o fmax2.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fmin2.c -o fmin2.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fprec.c -o fprec.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fround.c -o fround.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ftrunc.c -o ftrunc.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sign.c -o sign.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c fsign.c -o fsign.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c imax2.c -o imax2.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c imin2.c -o imin2.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c chebyshev.c -o chebyshev.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c log1p.c -o log1p.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgammacor.c -o lgammacor.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gammalims.c -o gammalims.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c stirlerr.c -o stirlerr.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bd0.c -o bd0.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gamma.c -o gamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lgamma.c -o lgamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c gamma_cody.c -o gamma_cody.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c beta.c -o beta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c lbeta.c -o lbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c polygamma.c -o polygamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c cospi.c -o cospi.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_i.c -o bessel_i.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_j.c -o bessel_j.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_k.c -o bessel_k.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c bessel_y.c -o bessel_y.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c choose.c -o choose.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c snorm.c -o snorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c sexp.c -o sexp.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgamma.c -o dgamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pgamma.c -o pgamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qgamma.c -o qgamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rgamma.c -o rgamma.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbeta.c -o dbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pbeta.c -o pbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qbeta.c -o qbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbeta.c -o rbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dunif.c -o dunif.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c punif.c -o punif.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qunif.c -o qunif.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c runif.c -o runif.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnorm.c -o dnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnorm.c -o pnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnorm.c -o qnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnorm.c -o rnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dlnorm.c -o dlnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plnorm.c -o plnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qlnorm.c -o qlnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlnorm.c -o rlnorm.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c df.c -o df.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pf.c -o pf.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qf.c -o qf.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rf.c -o rf.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnf.c -o dnf.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dt.c -o dt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pt.c -o pt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qt.c -o qt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rt.c -o rt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnt.c -o dnt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dchisq.c -o dchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pchisq.c -o pchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qchisq.c -o qchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rchisq.c -o rchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnchisq.c -o rnchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dbinom.c -o dbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pbinom.c -o pbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qbinom.c -o qbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rbinom.c -o rbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rmultinom.c -o rmultinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dcauchy.c -o dcauchy.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pcauchy.c -o pcauchy.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qcauchy.c -o qcauchy.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rcauchy.c -o rcauchy.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dexp.c -o dexp.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pexp.c -o pexp.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qexp.c -o qexp.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rexp.c -o rexp.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dgeom.c -o dgeom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pgeom.c -o pgeom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qgeom.c -o qgeom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rgeom.c -o rgeom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dhyper.c -o dhyper.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c phyper.c -o phyper.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qhyper.c -o qhyper.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rhyper.c -o rhyper.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnbinom.c -o dnbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnbinom.c -o pnbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnbinom.c -o qnbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rnbinom.c -o rnbinom.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dpois.c -o dpois.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ppois.c -o ppois.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qpois.c -o qpois.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rpois.c -o rpois.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dweibull.c -o dweibull.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pweibull.c -o pweibull.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qweibull.c -o qweibull.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rweibull.c -o rweibull.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dlogis.c -o dlogis.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c plogis.c -o plogis.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qlogis.c -o qlogis.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c rlogis.c -o rlogis.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnchisq.c -o dnchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnchisq.c -o pnchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnchisq.c -o qnchisq.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c dnbeta.c -o dnbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnbeta.c -o pnbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnbeta.c -o qnbeta.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnf.c -o pnf.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c pnt.c -o pnt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnf.c -o qnf.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qnt.c -o qnt.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c ptukey.c -o ptukey.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c qtukey.c -o qtukey.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c toms708.c -o toms708.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c wilcox.c -o wilcox.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c signrank.c -o signrank.lo
gcc -m64 -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fPIC  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -c std_unif.c -o std_unif.lo
gcc -m64 -std=gnu99 -shared -fopenmp -Wl,-z,relro  -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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[]\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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g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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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 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
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 See also the
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())
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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
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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
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cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
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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 
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
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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
Underfull \hbox (badness 1102) in paragraph at lines 6214--6227
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
Underfull \hbox (badness 1308) in paragraph at lines 6228--6236
[]\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
[94] [95]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6381--6381
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[96]
Overfull \hbox (107.35893pt too wide) in paragraph at lines 6423--6425
[]\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 : 
[97] [98]
Underfull \hbox (badness 10000) in paragraph at lines 6565--6568
[]\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 6565--6568
\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
[99] [100]
Underfull \hbox (badness 1248) in paragraph at lines 6747--6753
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
Underfull \hbox (badness 10000) in paragraph at lines 6767--6769
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[101]
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[102] [103]
Underfull \vbox (badness 10000) has occurred while \output is active [104]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7001--7001
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[105]
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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-
[106] [107] [108] [109]
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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
[110] [111]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7482--7482
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
Underfull \hbox (badness 4595) in paragraph at lines 7524--7527
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[112] [113] [114]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7720--7720
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[115] [116]
Underfull \hbox (badness 8132) in paragraph at lines 7821--7825
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7821--7825
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 7840--7850
[]\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 1062) in paragraph at lines 7840--7850
[][]\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
[117]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7872--7876
[]\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")
Underfull \hbox (badness 7451) in paragraph at lines 7911--7921
[][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-
Underfull \hbox (badness 3449) in paragraph at lines 7911--7921
\T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10
 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a
m-
[118] [119] [120] [121] [122] [123]
Underfull \hbox (badness 10000) in paragraph at lines 8340--8352
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8340--8352
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[124] [125] [126]
Underfull \hbox (badness 5802) in paragraph at lines 8567--8571
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
Underfull \hbox (badness 10000) in paragraph at lines 8602--8603
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8787--8791
[]\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
[130]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8875--8875
 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8877--8877
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
[131]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 8902--8902
 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 8903--8903
 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[132] [133]
Underfull \hbox (badness 5403) in paragraph at lines 9021--9023
[]\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 9040--9042
[]\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
[134]
Underfull \hbox (badness 1132) in paragraph at lines 9112--9119
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[135]
Underfull \hbox (badness 1603) in paragraph at lines 9248--9251
[]\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
[136] [137] [138] [139] [140] [141] [142] [143] [144]
Underfull \hbox (badness 1917) in paragraph at lines 9854--9859
[]\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
[145]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9909--9909
 []\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 9910--9910
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[146] [147]
Underfull \hbox (badness 1168) in paragraph at lines 10012--10017
\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 10051--10057
[]\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
Underfull \hbox (badness 5403) in paragraph at lines 10058--10061
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[148] [149] [150]
Underfull \hbox (badness 2828) in paragraph at lines 10217--10221
[][][]$\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 10217--10221
\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 / Double _
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10250--10250
 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[151] [152] [153] [154]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10465--10465
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[155]
Underfull \hbox (badness 1629) in paragraph at lines 10539--10543
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[156]
Underfull \hbox (badness 2150) in paragraph at lines 10640--10643
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[157]
Underfull \hbox (badness 3690) in paragraph at lines 10654--10662
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10663--10665
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
Underfull \hbox (badness 3735) in paragraph at lines 10683--10690
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[158] [159] [160]
Underfull \hbox (badness 10000) in paragraph at lines 10879--10882
[]\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
[161] [162] [163] [164] [165] [166] [167] [168] [169]
Underfull \hbox (badness 5288) in paragraph at lines 11576--11578
[]\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 11586--11591
[]\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
[170]
Underfull \hbox (badness 10000) in paragraph at lines 11646--11648
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[171] [172]
Underfull \hbox (badness 4569) in paragraph at lines 11763--11767
[]\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
Underfull \hbox (badness 2401) in paragraph at lines 11763--11767
\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
[173] [174]
Underfull \hbox (badness 10000) in paragraph at lines 11878--11880
[]\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
Underfull \hbox (badness 2790) in paragraph at lines 11921--11923
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[175] [176] [177]
Underfull \hbox (badness 4048) in paragraph at lines 12092--12102
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 12092--12102
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[178] [179] [180]
Underfull \hbox (badness 5460) in paragraph at lines 12340--12349
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[181] [182] [183] [184] [185]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12714--12714
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[186] [187] [188] [189]
Underfull \hbox (badness 5119) in paragraph at lines 12999--13002
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[190] [191]
Underfull \hbox (badness 2221) in paragraph at lines 13160--13169
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13421--13423
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[196] [197]
Underfull \hbox (badness 10000) in paragraph at lines 13536--13538
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 13686--13688
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13795--13799
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13806--13809
[][][]$\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[] 
[202]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[203]
Underfull \hbox (badness 10000) in paragraph at lines 13942--13945
[][][]\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 13952--13952
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[204]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14027--14027
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[205]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 7238) in paragraph at lines 14080--14087
[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 14080--14087
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 14080--14087
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 14088--14092
[]\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,
[206] [207] [208]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14251--14251
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14252--14252
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[209]
Underfull \hbox (badness 10000) in paragraph at lines 14331--14335
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 14331--14335
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[210] [211]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14479--14479
 []\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 14482--14482
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[212]
Underfull \hbox (badness 1168) in paragraph at lines 14566--14570
[]\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-
Underfull \hbox (badness 2012) in paragraph at lines 14566--14570
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[213]
Underfull \hbox (badness 6944) in paragraph at lines 14661--14664
[][][]\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 ,
[214]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14686--14686
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[215] [216]
Underfull \hbox (badness 10000) in paragraph at lines 14820--14822
[]\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
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14839--14839
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14841--14841
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14844--14844
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[] 
Underfull \hbox (badness 2790) in paragraph at lines 14850--14853
[]\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
[217]
Underfull \hbox (badness 4254) in paragraph at lines 14866--14874
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14881--14885
[]\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
[218]
Underfull \hbox (badness 10000) in paragraph at lines 14950--14952
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14956--14960
[]\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,
Underfull \hbox (badness 10000) in paragraph at lines 14956--14960
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 14961--14969
[]\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
Underfull \hbox (badness 3601) in paragraph at lines 14995--14999
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 14995--14999
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15062--15062
 []\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 ")[] 
[220]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15084--15084
 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[] 
[221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15902--15902
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[233]
Underfull \hbox (badness 2418) in paragraph at lines 16011--16015
\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 16018--16021
[]\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
Underfull \hbox (badness 2326) in paragraph at lines 16046--16053
[][][]\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 ,
[234] [235] [236] [237]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16292--16292
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 16317--16324
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16585--16585
 []  \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 [242]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16614--16614
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
[243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16665--16665
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 16671--16675
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16671--16675
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[244] [245] [246] [247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17030--17030
 []\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))) 
[248] [249] [250] [251]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17284--17284
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[252] [253] [254]
Underfull \hbox (badness 2435) in paragraph at lines 17545--17547
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[255]
Underfull \hbox (badness 1867) in paragraph at lines 17587--17594
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17587--17594
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
Underfull \hbox (badness 1490) in paragraph at lines 17587--17594
\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
Underfull \hbox (badness 2285) in paragraph at lines 17602--17604
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17610--17610
 []\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.[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17620--17620
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 
[256]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 17640--17640
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[257] [258]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17774--17774
 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 17780--17780
 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17783--17783
 []\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 17789--17789
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[259] [260]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17916--17916
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17924--17924
 []\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):[] 
[261] [262] [263]
Underfull \hbox (badness 10000) in paragraph at lines 18129--18131
[]\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
[264]
Underfull \hbox (badness 4217) in paragraph at lines 18213--18222
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18228--18244
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 4699) in paragraph at lines 18642--18645
[]\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 ,
[271] [272]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18765--18765
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[273] [274]
Underfull \hbox (badness 4739) in paragraph at lines 18900--18902
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[275] [276] [277] [278] [279] [280] [281]
Underfull \hbox (badness 1430) in paragraph at lines 19313--19318
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 19313--19318
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 19374--19379
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[283]
Underfull \hbox (badness 10000) in paragraph at lines 19434--19441
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 19434--19441
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 19434--19441
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with
Underfull \hbox (badness 5908) in paragraph at lines 19434--19441
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 19450--19452
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[284]
Underfull \hbox (badness 1975) in paragraph at lines 19522--19525
[]\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
[285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1077) in paragraph at lines 19917--19922
[]\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
[291]
Underfull \hbox (badness 10000) in paragraph at lines 19931--19938
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20005--20009
[]\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-tory
[293]
Underfull \hbox (badness 10000) in paragraph at lines 20135--20139
[]\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 20135--20139
[][]\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
[294] [295]
Underfull \hbox (badness 10000) in paragraph at lines 20233--20240
[][][]\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 ,
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20354--20358
[]\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
[298]
Underfull \hbox (badness 5161) in paragraph at lines 20424--20429
[]\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 20424--20429
\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 20424--20429
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20424--20429
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[299] [300]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20591--20591
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20595--20595
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[301]
Underfull \hbox (badness 3343) in paragraph at lines 20651--20655
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20737--20737
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20748--20748
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[303] [304]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20859--20859
 []\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 20862--20862
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
[305]
Underfull \hbox (badness 6380) in paragraph at lines 20907--20912
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
Underfull \hbox (badness 1337) in paragraph at lines 20965--20972
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 1960) in paragraph at lines 20965--20972
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or
Underfull \hbox (badness 1043) in paragraph at lines 20965--20972
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
[306]
Underfull \hbox (badness 2564) in paragraph at lines 20985--20988
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21015--21015
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[307]
Underfull \hbox (badness 1205) in paragraph at lines 21038--21043
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[308]
Underfull \hbox (badness 1400) in paragraph at lines 21183--21187
[][][]\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
[309]
Overfull \hbox (36.83002pt too wide) in paragraph at lines 21203--21210
[]\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo
gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ;
Underfull \hbox (badness 4886) in paragraph at lines 21203--21210
\T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m
/n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the
[310] [311]
Underfull \hbox (badness 2469) in paragraph at lines 21353--21359
[]\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. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 21353--21359
\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 names.
Underfull \hbox (badness 10000) in paragraph at lines 21353--21359
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[312] [313] [314] [315]
Underfull \hbox (badness 10000) in paragraph at lines 21670--21672
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[316] [317] [318] [319] [320]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 21974--21974
 []\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 21975--21975
 []        \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 21978--21978
 []\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)[] 
[321] [322]
Underfull \hbox (badness 1655) in paragraph at lines 22102--22106
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[323] [324] [325] [326]
Underfull \hbox (badness 2277) in paragraph at lines 22351--22354
[]\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.
[327] [328] [329] [330] [331] [332] [333]
Underfull \hbox (badness 10000) in paragraph at lines 22836--22842
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22836--22842
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[334]
Underfull \hbox (badness 1484) in paragraph at lines 22868--22876
[]\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 2951) in paragraph at lines 22868--22876
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22868--22876
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[335]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22945--22945
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[336]
Underfull \hbox (badness 10000) in paragraph at lines 22999--23003
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 22999--23003
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 10000) in paragraph at lines 23450--23458
\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 ;
[343] [344]
Underfull \hbox (badness 3849) in paragraph at lines 23564--23569
[]\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
[345]
Underfull \hbox (badness 7308) in paragraph at lines 23641--23647
[]\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 5077) in paragraph at lines 23641--23647
\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 10000) in paragraph at lines 23651--23654
[]\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 23651--23654
\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
[346] [347]
Underfull \hbox (badness 10000) in paragraph at lines 23803--23805
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[348] [349] [350]
Underfull \hbox (badness 6188) in paragraph at lines 24022--24025
[]\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
[351] [352] [353] [354] [355] [356] [357]
Underfull \hbox (badness 2197) in paragraph at lines 24494--24498
[]\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 24494--24498
\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
[358]
Underfull \hbox (badness 2846) in paragraph at lines 24508--24512
[]\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-
Underfull \hbox (badness 1990) in paragraph at lines 24508--24512
\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
[359]
Underfull \hbox (badness 10000) in paragraph at lines 24601--24607
[]\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 24601--24607
\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 24614--24616
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24665--24665
 [] \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:[] 
[361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24858--24864
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 24858--24864
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24858--24864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[364]
Underfull \hbox (badness 4120) in paragraph at lines 24944--24951
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[365] [366]
Underfull \hbox (badness 1694) in paragraph at lines 25080--25083
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[367] [368] [369]
Underfull \hbox (badness 1603) in paragraph at lines 25327--25329
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[370] [371]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 25450--25458
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[372]
Underfull \hbox (badness 5475) in paragraph at lines 25587--25597
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
[373]
Underfull \hbox (badness 3271) in paragraph at lines 25629--25632
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 25644--25646
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[374] [375] [376]
Underfull \hbox (badness 3138) in paragraph at lines 25907--25913
[]\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 25907--25913
\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 25907--25913
\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
Underfull \hbox (badness 1194) in paragraph at lines 25920--25923
[]\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 25944--25946
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 25956--25960
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25956--25960
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 25961--25967
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
[377]
Underfull \hbox (badness 3826) in paragraph at lines 25976--25981
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 25982--25993
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 25994--25997
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 26004--26016
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 1072) in paragraph at lines 26004--26016
[][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar
e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a
Underfull \hbox (badness 10000) in paragraph at lines 26018--26025
[]\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 10000) in paragraph at lines 26018--26025
\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
Underfull \hbox (badness 6380) in paragraph at lines 26018--26025
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 26018--26025
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[378] [379] [380] [381] [382]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26349--26349
 []\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 26362--26366
[]\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 26362--26366
\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)]
[383] [384] [385] [386] [387]
Underfull \hbox (badness 4341) in paragraph at lines 26686--26688
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 26722--26728
[][][]\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
[388]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26744--26744
 []\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 26756--26756
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27190--27194
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[396]
Underfull \hbox (badness 1796) in paragraph at lines 27256--27259
[]\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
[397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27453--27456
[]\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
[400] [401] [402] [403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1226) in paragraph at lines 28085--28090
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[409]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28130--28130
 []           \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))[] 
[410] [411] [412] [413]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28396--28396
 []\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 28407--28407
 []\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 28413--28413
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28414--28414
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28417--28417
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[414]
Underfull \hbox (badness 7415) in paragraph at lines 28492--28496
[]\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
[415]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28513--28513
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[416] [417]
Underfull \hbox (badness 2418) in paragraph at lines 28672--28683
[]\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
[418]
Underfull \hbox (badness 1248) in paragraph at lines 28806--28813
\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 28806--28813
\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 /
[419] [420]
Underfull \hbox (badness 1533) in paragraph at lines 28917--28920
[]\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
[421]
Underfull \hbox (badness 1337) in paragraph at lines 29014--29017
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[422]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29062--29062
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 29080--29091
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 29092--29095
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[423] [424]
Underfull \hbox (badness 1117) in paragraph at lines 29187--29193
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[425] [426] [427] [428] [429] [430]
Underfull \hbox (badness 4048) in paragraph at lines 29565--29570
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
Underfull \hbox (badness 4582) in paragraph at lines 29565--29570
\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 29565--29570
\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 ,
[431] [432] [433] [434] [435] [436] [437] [438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30111--30111
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[439] [440] [441] [442]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 30397--30399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[443] [444] [445]
Underfull \hbox (badness 7558) in paragraph at lines 30613--30617
[]\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 30623--30625
[]\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 5417) in paragraph at lines 30628--30631
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 30632--30634
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 30635--30637
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 10000) in paragraph at lines 31040--31044
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[452] [453] [454] [455] [456]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31371--31371
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31374--31374
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[457] [458] [459]
Underfull \hbox (badness 3375) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/
ptm/m/n/10 , are in-valid, e.g., du-
Underfull \hbox (badness 2359) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is 
back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal
Underfull \hbox (badness 2582) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m
atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call
[460] [461] [462]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 31755--31755
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[463] [464]
Underfull \hbox (badness 10000) in paragraph at lines 31886--31890
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 31886--31890
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[465] [466] [467]
Underfull \hbox (badness 2302) in paragraph at lines 32137--32144
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[468]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32189--32189
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[469]
Underfull \hbox (badness 1158) in paragraph at lines 32293--32298
[]\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
[470]
Underfull \hbox (badness 10000) in paragraph at lines 32320--32326
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 32320--32326
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[471]
Underfull \hbox (badness 10000) in paragraph at lines 32396--32401
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 32396--32401
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[472]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32478--32478
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[473] [474] [475]
Underfull \hbox (badness 2809) in paragraph at lines 32742--32748
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 32749--32752
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487]
Underfull \hbox (badness 1735) in paragraph at lines 33554--33560
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[488]
Underfull \hbox (badness 4303) in paragraph at lines 33570--33573
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[489] [490] [491] [492]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 33888--33888
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[493] [494] [495] [496]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34140--34140
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34142--34142
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[497]
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
[][][]\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
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
\T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T
1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
\T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i
s the de-fault cur-rently;
Underfull \hbox (badness 2512) in paragraph at lines 34200--34202
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[498]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34296--34296
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[499] [500] [501]
Underfull \vbox (badness 10000) has occurred while \output is active [502]
[503]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34624--34624
 []\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 34639--34639
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[504] [505] [506] [507] [508] [509]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35078--35078
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35079--35079
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[510] [511] [512] [513]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35343--35343
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[514]
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
[]\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 '
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 35427--35437
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
Underfull \hbox (badness 5189) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
Underfull \hbox (badness 4193) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[515]
Underfull \hbox (badness 10000) in paragraph at lines 35471--35477
[]\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 35471--35477
\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 35471--35477
\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 1728) in paragraph at lines 35483--35490
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 35483--35490
\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 35483--35490
\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
[516] [517] [518] [519] [520]
Underfull \hbox (badness 10000) in paragraph at lines 35824--35830
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[521] [522] [523]
Underfull \hbox (badness 1163) in paragraph at lines 36012--36019
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 36012--36019
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[524] [525] [526] [527]
Underfull \hbox (badness 1142) in paragraph at lines 36275--36281
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36290--36290
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[528] [529] [530]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36538--36538
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[531]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36582--36582
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[532] [533] [534] [535] [536] [537] [538]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37016--37016
 []\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 37019--37019
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[539]
Underfull \hbox (badness 10000) in paragraph at lines 37070--37077
[]\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 37070--37077
\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 ).
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37121--37121
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[540] [541] [542] [543]
Underfull \hbox (badness 2762) in paragraph at lines 37360--37369
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 37360--37369
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple
[544]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 37422--37422
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[545] [546]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37587--37587
 []\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. 
[547]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 37625--37625
 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
[548]
Underfull \hbox (badness 3219) in paragraph at lines 37674--37679
[]\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 37674--37679
\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
[549]
Underfull \hbox (badness 2452) in paragraph at lines 37764--37767
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 37764--37767
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 37951--37955
[]\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
Underfull \hbox (badness 1584) in paragraph at lines 37966--37969
[]\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
[553] [554]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38098--38098
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38168--38168
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[556] [557] [558]
Underfull \hbox (badness 1082) in paragraph at lines 38306--38309
[]\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
[559] [560]
Underfull \hbox (badness 1038) in paragraph at lines 38493--38496
[]\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
[561] [562] [563] [564] [565] [566]
Underfull \hbox (badness 1515) in paragraph at lines 38857--38860
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[567] [568] [569]
Underfull \hbox (badness 4096) in paragraph at lines 39098--39101
[]\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 ,
[570] [571]
Underfull \hbox (badness 10000) in paragraph at lines 39212--39216
[]\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.,
[572] [573]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 39365--39365
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 39367--39367
 []            \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 39369--39369
 []                 \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[] 
[574]
Underfull \hbox (badness 10000) in paragraph at lines 39382--39384
[]\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
[575]
Underfull \hbox (badness 10000) in paragraph at lines 39462--39465
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[576] [577]
Underfull \hbox (badness 1867) in paragraph at lines 39580--39584
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 39642--39646
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[578] [579] [580] [581] [582] [583] [584]
Underfull \hbox (badness 10000) in paragraph at lines 40060--40067
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40116--40125
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40116--40125
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40126--40134
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40126--40134
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 1303) in paragraph at lines 40126--40134
\T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by
 de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[585]
Underfull \hbox (badness 1337) in paragraph at lines 40192--40200
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40201--40204
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[586]
Underfull \hbox (badness 4429) in paragraph at lines 40258--40260
[][][]$\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 40267--40267
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[587] [588] [589]
Underfull \hbox (badness 10000) in paragraph at lines 40484--40486
[]\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
[590] [591]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40606--40606
 []\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 40608--40608
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [592]
[593] [594] [595] [596]
Underfull \hbox (badness 6542) in paragraph at lines 40970--40972
[]\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
[597] [598] [599]
Underfull \hbox (badness 3460) in paragraph at lines 41136--41139
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via
Underfull \hbox (badness 1708) in paragraph at lines 41143--41151
[]\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 41143--41151
\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
Underfull \hbox (badness 10000) in paragraph at lines 41152--41156
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 41152--41156
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 41152--41156
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 41173--41178
[][][]\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;
[600]
Underfull \hbox (badness 3895) in paragraph at lines 41235--41247
[]\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 41235--41247
\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 ,
[601] [602] [603]
Underfull \hbox (badness 10000) in paragraph at lines 41420--41423
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[604] [605]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 41557--41557
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[606] [607] [608] [609] [610] [611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42024--42024
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 42033--42033
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[613]
Underfull \hbox (badness 1803) in paragraph at lines 42150--42153
[]\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 2334) in paragraph at lines 42154--42161
[]\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
[614]
Underfull \hbox (badness 4726) in paragraph at lines 42180--42184
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 42180--42184
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[615] [616]
Underfull \hbox (badness 3668) in paragraph at lines 42369--42371
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[617] [618]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 42473--42473
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[619]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42548--42548
 []\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[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 42556--42556
 []\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 ...[] 
[620] [621]
Underfull \hbox (badness 6220) in paragraph at lines 42686--42691
[]\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 42686--42691
\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 1533) in paragraph at lines 42686--42691
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
Underfull \hbox (badness 6592) in paragraph at lines 42702--42707
[]\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
[622]
Underfull \hbox (badness 1603) in paragraph at lines 42721--42725
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[623]
Underfull \hbox (badness 10000) in paragraph at lines 42786--42789
[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
Underfull \hbox (badness 10000) in paragraph at lines 42786--42789
\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 2818) in paragraph at lines 42792--42798
[]\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
Overfull \hbox (15.18042pt too wide) in paragraph at lines 42827--42827
 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[624] [625]
Underfull \hbox (badness 1622) in paragraph at lines 42921--42923
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[626] [627] [628] [629]
Underfull \hbox (badness 10000) in paragraph at lines 43189--43194
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
Underfull \hbox (badness 10000) in paragraph at lines 43189--43194
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
Underfull \hbox (badness 10000) in paragraph at lines 43189--43194
\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[630]
Underfull \hbox (badness 2846) in paragraph at lines 43281--43285
[]\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
[631]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 43321--43321
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
Underfull \hbox (badness 3209) in paragraph at lines 43342--43346
[]\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
[632]) (./compiler-pkg.tex
Chapter 2.
[633]
Underfull \hbox (badness 2884) in paragraph at lines 101--115
[]\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 101--115
\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
[634] [635] [636]) (./datasets-pkg.tex
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[637] [638] [639] [640] [641]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[642]
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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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[644] [645] [646] [647]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[648] [649]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[650] [651]
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[]\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.
[652] [653]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[654] [655] [656] [657] [658]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[659] [660]
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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
[661] [662] [663]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[664]
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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)[] 
[665] [666]
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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]]))))[] 
[667] [668] [669] [670]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[671] [672] [673] [674] [675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[679]
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[680]
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[682]
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[683] [684]
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[685]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[686] [687] [688] [689] [690] [691] [692]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[693] [694]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[695]
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[696]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
 datasets .
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[697]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
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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 /
[698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709]
[710] [711]) (./grDevices-pkg.tex [712]
Chapter 4.
[713] [714] [715] [716] [717] [718]
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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/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[719]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[720] [721] [722] [723] [724] [725] [726] [727] [728]
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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
[729]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[730]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
[731]
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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[732]
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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
[733] [734] [735]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[736]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
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[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[737] [738] [739]
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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
[740]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
[741]
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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 ,
[742]
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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
[743] [744]
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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
[745] [746]
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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
[747] [748]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
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[750] [751] [752] [753] [754]
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[756] [757] [758] [759] [760]
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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))[] 
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[761]
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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
[762] [763] [764]
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 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[765]
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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
[766]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[767] [768] [769] [770]
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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 ,
[771] [772] [773] [774] [775]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[776]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[778]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[779] [780]
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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
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[781]
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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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[782]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[783]
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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
[784] [785]
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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
[786] [787]
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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
[788]
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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
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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 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[789] [790]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[791]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[792] [793]
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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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[794] [795] [796] [797] [798]
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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
[799] [800] [801] [802] [803] [804] [805]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[806]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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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
[807]
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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
[808]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[809]
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[810]
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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 /
[811] [812] [813]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via
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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
[814] [815] [816]) (./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
[817] [818] [819] [820]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[821] [822] [823]
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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
[824] [825] [826]
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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
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[827]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[828] [829]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[830] [831] [832] [833] [834] [835] [836]
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 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 
[837]
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\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 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, 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 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[838]
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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)[] 
[839] [840] [841] [842] [843]
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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
[844]
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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 = "")[] 
[845]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[846] [847]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, 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))[] 
[848] [849] [850] [851] [852]
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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
[853] [854] [855] [856] [857]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[858] [859]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[860]
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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 :[] 
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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
[861]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[862] [863] [864]
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 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
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 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[865]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[866]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[867] [868] [869]
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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"),[] 
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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[870] [871] [872]
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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])[] 
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 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 
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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 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
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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
[875] [876]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[877]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[878] [879]
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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
[880] [881] [882] [883]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[884]
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\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
[885]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 
[886]
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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))[] 
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[887]
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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 ,
[888] [889]
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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.
[890] [891]
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<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"mai.pdf, id=1554
9, 289.08pt x 289.08pt>
<use "/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"mai.pdf>
[892 </builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/mai.pdf>]
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<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"oma.pdf, id=1556
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<use "/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"oma.pdf>
[893 </builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/oma.pdf>]
[894]
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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
[895]
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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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[897]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[898] [899] [900] [901]
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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)[] 
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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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[902] [903] [904] [905] [906] [907] [908]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6064--6064
 []\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[] 
[909] [910] [911] [912] [913] [914]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[915] [916]
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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
<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"pch.pdf, id=1600
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<use "/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"pch.pdf>
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[][] 
[917 </builddir/build/BUILD/R-3.5.0/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,[] 
[918]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[920]
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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)))))[] 
[921]
Underfull \hbox (badness 2600) in paragraph at lines 6974--6976
[]\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
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[925]
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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))[] 
[926] [927] [928] [929] [930] [931]
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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):[] 
[932]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
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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,[] 
[938]
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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[939] [940]
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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, ...)[] 
[941] [942]
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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
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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),[] 
[945] [946]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[947] [948]
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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�...")[] 
[949]
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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
[950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8789 \HeaderA{units}{Graphical Units}{units}
                                               [951]
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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
[952] [953]
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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)[] 
[954]) (./grid-pkg.tex
Chapter 6.
[955] [956] [957] [958] [959] [960]
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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/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 
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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-
[972] [973] [974]
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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(...)))[] 
[982] [983] [984]
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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")[] 
[985]
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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 ,
[986]
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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
[987] [988] [989]
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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
[990] [991] [992]
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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-
[993] [994] [995]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[996] [997] [998] [999]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1000] [1001] [1002] [1003] [1004]
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1005]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[1006]
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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
[1007] [1008]
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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,[] 
[1009] [1010] [1011]
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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")[] 
[1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022]
[1023] [1024]
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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
[1025]
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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-
[1026] [1027] [1028]
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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
[1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037]
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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
[1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047]
Underfull \hbox (badness 3449) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1048] [1049] [1050] [1051] [1052]
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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
[1053]
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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 ,
[1054] [1055]
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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
[1056] [1057] [1058]
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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"))))[] 
[1059]) (./methods-pkg.tex [1060]
Chapter 7.
[1061] [1062]
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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
[1063] [1064] [1065]
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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-
[1066] [1067]
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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[] 
[1068]
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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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[1071]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
 Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] 
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
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\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082]
[1083] [1084]
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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/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
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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
[1087] [1088] [1089]
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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 =
[1090] [1091]
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1092] [1093] [1094]
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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
[1095]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1096] [1097] [1098]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1099] [1100] [1101] [1102] [1103] [1104] [1105]
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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
[1106] [1107]
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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
[1108]
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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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[]
[1109] [1110]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
[1111]
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[]\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = 
"Pos") 
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
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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
[1112] [1113] [1114]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1115] [1116]
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\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1117]
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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,[] 
[1118]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1119] [1120]
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\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1121]
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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 ,
[1122] [1123] [1124]
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
[1125] [1126] [1127] [1128]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1129]
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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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[1131]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1132]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1133]
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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
[1134] [1135] [1136]
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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
[1137]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1138]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 10000) in paragraph at lines 6210--6226
[]\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
[1143] [1144]
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
[1145]
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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
[1146]
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[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1147]
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][]\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
[1148]
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[1150] [1151]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}
                               [1152]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
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\T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the 
S4 bit of the ob-ject. With
[1153] [1154]
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")[] 
[1155]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
[1156]
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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 ,
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 ,
[1157] [1158]
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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
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[]\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
[1159] [1160]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171]
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
[1172]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1173]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1174] [1175] [1176] [1177]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1178] [1179] [1180]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1181] [1182]
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 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1184] [1185] [1186] [1187]
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 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1188]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1189]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198]
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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.,
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
[1199] [1200] [1201] [1202]) (./parallel-pkg.tex
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
[1203]
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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
[1204] [1205]
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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
[1206]
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[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1207] [1208]
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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
[1209] [1210] [1211] [1212]
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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
Underfull \hbox (badness 1178) in paragraph at lines 742--751
\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
[1213] [1214]
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 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1215]
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[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1216]
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 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
[1217]
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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1218]
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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
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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
[1219]
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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)[] 
[1220] [1221]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296
 []                 \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")))[] 
Underfull \hbox (badness 1577) in paragraph at lines 1339--1342
[]\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
[1222]
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[]\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
[1223] [1224]) (./splines-pkg.tex
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
[1225] [1226] [1227] [1228] [1229] [1230] [1231]
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 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1232] [1233] [1234] [1235]
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 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1236] [1237] [1238]) (./stats-pkg.tex
Chapter 10.
[1239]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\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 ,
[1240] [1241] [1242] [1243] [1244]
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 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1245] [1246] [1247] [1248] [1249] [1250] [1251]
Underfull \hbox (badness 1024) in paragraph at lines 847--849
[]\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
[1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 1391--1393
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1260]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1261] [1262] [1263] [1264]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via
Underfull \hbox (badness 2197) in paragraph at lines 1773--1777
\T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-
[1265] [1266]
Underfull \hbox (badness 4303) in paragraph at lines 1874--1876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues,
 see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/
pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with
[1267] [1268] [1269]
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2096--2101
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2102--2108
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1270] [1271]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1272] [1273] [1274]
Underfull \hbox (badness 1221) in paragraph at lines 2457--2462
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2457--2462
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1275]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1276] [1277]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1278] [1279] [1280] [1281]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1282] [1283] [1284]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 
[1285]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176
 []\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 3177--3177
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1286]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1287] [1288] [1289] [1290] [1291]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1292] [1293] [1294] [1295]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1296] [1297] [1298] [1299] [1300]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135
 []\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 4136--4136
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1301] [1302] [1303]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1304] [1305] [1306]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1307]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\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 =
[1308] [1309]
Underfull \hbox (badness 2080) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
Underfull \hbox (badness 2050) in paragraph at lines 4757--4763
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex-
ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me
th-ods, and \T1/pcr/m/n/10 coef
Underfull \hbox (badness 4954) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes
 should typ-i-cally also keep the \T1/pcr/m/n/10 complete = *
Underfull \hbox (badness 4726) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe
f(obj, complete = TF))\T1/ptm/m/n/10 ,
[1310] [1311] [1312] [1313]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019
 []\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 5021--5021
 []\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))[] 
[1314]
Underfull \hbox (badness 7397) in paragraph at lines 5108--5112
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5108--5112
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1315] [1316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242
 []\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 5260--5260
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
Underfull \hbox (badness 2680) in paragraph at lines 5287--5289
[]\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
[1317]
Underfull \hbox (badness 10000) in paragraph at lines 5292--5294
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1318] [1319]
Underfull \hbox (badness 1436) in paragraph at lines 5470--5475
[]\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 5470--5475
\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 5470--5475
\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 ,
[1320] [1321] [1322]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5669--5669
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1323]
Underfull \hbox (badness 1168) in paragraph at lines 5741--5746
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1324] [1325]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5836--5836
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1326] [1327] [1328]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6021--6021
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1329] [1330]
Underfull \hbox (badness 10000) in paragraph at lines 6184--6189
[]\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
[1331] [1332] [1333]
Underfull \hbox (badness 5954) in paragraph at lines 6380--6382
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1334]
Underfull \hbox (badness 2503) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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 6469--6474
\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,
[1335]
Underfull \hbox (badness 7238) in paragraph at lines 6505--6508
[][][]\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
[1336]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6540--6540
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6555--6555
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6570--6570
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1337] [1338] [1339] [1340]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6814--6814
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1341] [1342]
Underfull \vbox (badness 10000) has occurred while \output is active [1343]
[1344] [1345] [1346]
Underfull \hbox (badness 10000) in paragraph at lines 7212--7216
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1347]
Underfull \hbox (badness 6493) in paragraph at lines 7311--7314
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1348] [1349]
Underfull \hbox (badness 10000) in paragraph at lines 7448--7451
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1350] [1351] [1352] [1353] [1354] [1355]
Underfull \hbox (badness 10000) in paragraph at lines 7858--7863
[]\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 , ...,
[1356] [1357]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7996--7998
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1358] [1359] [1360]
Underfull \hbox (badness 1210) in paragraph at lines 8213--8215
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8664--8664
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8686--8686
 []\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 8689--8689
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1368] [1369]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8827--8827
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1370]
Underfull \hbox (badness 1859) in paragraph at lines 8866--8871
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1371] [1372] [1373]
Underfull \hbox (badness 2865) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-
Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1374] [1375]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9254--9254
 []           \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 9255--9255
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1376] [1377] [1378]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9434--9436
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1379] [1380] [1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 2443) in paragraph at lines 9887--9893
[][][]\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);
[1386] [1387] [1388]
Underfull \hbox (badness 3758) in paragraph at lines 10100--10103
[]\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
[1389] [1390] [1391] [1392]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10336--10336
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1393]
Underfull \hbox (badness 4132) in paragraph at lines 10401--10405
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1394]
Underfull \hbox (badness 10000) in paragraph at lines 10506--10509
[]\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
[1395] [1396] [1397]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\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 ^^@
[1398]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1399]
Underfull \hbox (badness 10000) in paragraph at lines 10833--10839
[][][]\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 10871--10876
\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 (=
[1400] [1401]
Underfull \hbox (badness 2635) in paragraph at lines 11004--11007
\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
[1402] [1403] [1404]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 11208--11217
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 11208--11217
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1405]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11290--11290
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1406]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11323--11323
 []            \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 11336--11340
[]\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
[1407] [1408] [1409]
Underfull \hbox (badness 7379) in paragraph at lines 11516--11519
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1410] [1411]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11655--11655
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1412]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11723--11723
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11735--11735
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
[1413]
Underfull \hbox (badness 1062) in paragraph at lines 11784--11789
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11801--11803
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1414] [1415]
Underfull \hbox (badness 3623) in paragraph at lines 11955--11957
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1416] [1417]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12051--12051
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1418]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12144--12144
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 12192--12195
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1420] [1421] [1422]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12394--12396
[]\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
[1423]
Underfull \hbox (badness 4739) in paragraph at lines 12417--12419
[]\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
[1424]
Underfull \hbox (badness 2753) in paragraph at lines 12486--12488
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1425] [1426]
Underfull \hbox (badness 1292) in paragraph at lines 12611--12615
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1427]
Underfull \hbox (badness 10000) in paragraph at lines 12724--12726
[]\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
Underfull \hbox (badness 2894) in paragraph at lines 12730--12734
[]\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 12730--12734
\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
[1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13437--13437
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1439]
Underfull \hbox (badness 4518) in paragraph at lines 13480--13485
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1440] [1441]
Underfull \hbox (badness 10000) in paragraph at lines 13679--13683
[]\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
 ,
[1442] [1443] [1444]
Underfull \hbox (badness 6995) in paragraph at lines 13864--13866
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1445] [1446]
Underfull \hbox (badness 1163) in paragraph at lines 14012--14020
\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 ,
[1447] [1448]
Underfull \hbox (badness 4518) in paragraph at lines 14132--14137
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1449] [1450]
Underfull \hbox (badness 10000) in paragraph at lines 14270--14274
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 14270--14274
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1451]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14318--14318
 []\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 14319--14319
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1452]
Underfull \hbox (badness 10000) in paragraph at lines 14374--14377
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14374--14377
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1453] [1454] [1455] [1456]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14662--14662
 []\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 14663--14663
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1457]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14713--14715
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14756--14756
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 2726) in paragraph at lines 15163--15166
[]\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 ,
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15878--15878
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1476] [1477]
Underfull \hbox (badness 1014) in paragraph at lines 16016--16021
\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
[1478]
Underfull \hbox (badness 1648) in paragraph at lines 16082--16084
[]\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 16096--16105
\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 16096--16105
\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
[1479]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16164--16164
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16718--16718
 []\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[] 
[1489] [1490] [1491]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16946--16946
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Underfull \hbox (badness 2359) in paragraph at lines 17507--17509
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1501]
Underfull \vbox (badness 10000) has occurred while \output is active [1502]
Underfull \vbox (badness 10000) has occurred while \output is active [1503]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17679--17679
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1504]
Underfull \hbox (badness 10000) in paragraph at lines 17759--17763
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1505]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17839--17839
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17886--17886
 []\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 17933--17933
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514]
Underfull \hbox (badness 1248) in paragraph at lines 18424--18427
[]\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 1127) in paragraph at lines 18437--18441
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1515]
Underfull \hbox (badness 1478) in paragraph at lines 18445--18449
\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
Underfull \hbox (badness 2042) in paragraph at lines 18503--18505
[]\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
[1516] [1517]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18609--18609
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18651--18651
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18669--18669
 []\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 18672--18672
 []\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 18692--18692
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 18695--18695
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1519]
Underfull \hbox (badness 2564) in paragraph at lines 18730--18741
[]\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 18730--18741
\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
[1520]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18793--18793
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1521] [1522] [1523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19018--19018
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1524]
Underfull \hbox (badness 1337) in paragraph at lines 19094--19097
[]\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
[1525] [1526] [1527] [1528] [1529] [1530]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19413--19413
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1531]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19501--19501
 []       \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 (6.78088pt too wide) in paragraph at lines 19504--19504
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1532]
Underfull \hbox (badness 3049) in paragraph at lines 19583--19587
[]\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
[1533] [1534] [1535] [1536]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19831--19831
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 4779) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19841--19844
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1537]
Underfull \hbox (badness 1107) in paragraph at lines 19899--19901
[]\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
[1538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19954--19954
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1539]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19961--19961
 []\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)[] 
Underfull \hbox (badness 10000) in paragraph at lines 20011--20014
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 20011--20014
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1540]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20055--20055
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1541] [1542]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20180--20180
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1543]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20245
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1544]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20291--20291
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
Underfull \hbox (badness 10000) in paragraph at lines 20346--20348
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1545]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20383--20383
 [] \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 20388--20388
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556]
[1557] [1558]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21238--21238
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1559]
Underfull \hbox (badness 6859) in paragraph at lines 21305--21312
[][][]\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 21316--21322
[]\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 ,
[1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570]
[1571]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22054--22054
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1572] [1573] [1574] [1575] [1576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22338--22338
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22339--22339
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1577] [1578] [1579] [1580] [1581]
Underfull \hbox (badness 1337) in paragraph at lines 22662--22668
[]\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
[1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23214--23214
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1590] [1591]
Underfull \hbox (badness 1028) in paragraph at lines 23355--23358
[]\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
[1592] [1593]
Underfull \hbox (badness 10000) in paragraph at lines 23465--23468
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 23465--23468
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
Underfull \hbox (badness 10000) in paragraph at lines 23520--23522
[]\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
[1594]
Underfull \hbox (badness 10000) in paragraph at lines 23582--23584
[]\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
[1595] [1596]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23684--23684
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1597] [1598] [1599]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23904--23904
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1600] [1601] [1602]
Underfull \hbox (badness 10000) in paragraph at lines 24050--24053
[]\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
Underfull \hbox (badness 2134) in paragraph at lines 24102--24106
[][][]\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
[1603]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24115--24115
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1604] [1605] [1606] [1607] [1608] [1609] [1610]
Underfull \hbox (badness 6268) in paragraph at lines 24581--24586
[][]\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 ,
[1611]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24609--24609
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1612] [1613]
Underfull \hbox (badness 1867) in paragraph at lines 24786--24788
[]\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 24799--24803
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 24799--24803
\T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1614]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24835--24835
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1615] [1616] [1617]
Underfull \hbox (badness 2495) in paragraph at lines 25025--25034
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1618]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25107--25107
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
Underfull \hbox (badness 1412) in paragraph at lines 25114--25116
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1619]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25201--25201
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
[1620]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25226--25226
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25229--25229
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1621]
Underfull \hbox (badness 10000) in paragraph at lines 25271--25276
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 25271--25276
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1622]
Underfull \hbox (badness 2980) in paragraph at lines 25416--25418
[]\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g
iven, un-less it has been given as
[1623]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25452--25452
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25501--25501
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
[1624]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25522--25522
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1625]
[1626]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25626--25626
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1627]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25693--25693
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1628] [1629] [1630] [1631] [1632] [1633]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26072--26072
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
Underfull \hbox (badness 6477) in paragraph at lines 26126--26129
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1634] [1635]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26257--26257
 []\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 26258--26258
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1636]
Underfull \hbox (badness 2922) in paragraph at lines 26327--26332
[]\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
[1637]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26364--26364
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26367--26367
 []                    \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 26376--26376
 []         \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 26377--26377
 []  \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 26381--26381
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1638]
Underfull \hbox (badness 2922) in paragraph at lines 26423--26428
[]\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
Underfull \hbox (badness 3240) in paragraph at lines 26435--26438
[][][]\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 26456--26456
 []  \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 26459--26459
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1639]
Underfull \hbox (badness 2922) in paragraph at lines 26509--26514
[]\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
[1640]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26542--26542
 []  \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 26546--26546
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26556--26556
 []  \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 26561--26561
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1641]
Underfull \hbox (badness 2922) in paragraph at lines 26597--26603
[]\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 26619--26619
 []\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 26635--26635
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1642] [1643]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26749--26749
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1644]
Underfull \hbox (badness 2922) in paragraph at lines 26811--26816
[]\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
[1645]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26849--26849
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1646]
Underfull \hbox (badness 2922) in paragraph at lines 26898--26903
[]\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 26929--26929
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
[1647]
Underfull \hbox (badness 2922) in paragraph at lines 26963--26968
[]\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 (25.98041pt too wide) in paragraph at lines 26988--26988
 []\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)[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27012--27012
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 
[1648]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27022--27022
 []  \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 27057--27062
[]\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
[1649]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27079--27079
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 27097--27097
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1650]
Underfull \hbox (badness 6493) in paragraph at lines 27149--27154
[]\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 27176--27176
 []\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 27178--27178
 []\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 27181--27181
 []\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 27184--27184
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
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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
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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
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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
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 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
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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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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
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main = t.tit,[] 
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mon",[] 
[1681]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
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[1682]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1683]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
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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
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 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1694]
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
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[1695] [1696] [1697] [1698]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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v = FALSE,[] 
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 = 0)[] 
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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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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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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-
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[1713]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
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ALSE, 
[1719]
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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
[1720]
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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 "")[] 
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 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1721]) (./stats4-pkg.tex [1722]
Chapter 11.
[1723] [1724] [1725]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1726] [1727] [1728]pdfTeX warning (ext4): destination with the same identifier
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1730] [1731]) (./tcltk-pkg.tex [1732]
Chapter 12.
[1733] [1734] [1735] [1736]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1752]) (./tools-pkg.tex
Chapter 13.
[1753]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
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[1754]
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
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[1755]
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[1756]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
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[1757]
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ngle = TRUE, 
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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xz"),[] 
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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1767] [1768]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1769]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
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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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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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tm/m/n/10 and
[1771]
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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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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
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To"),[] 
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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/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
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[1785]
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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}",[] 
[1786]
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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
[1787]
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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
[1788]
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
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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 .
[1789]
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 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 
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", "Suggests"),[] 
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 = TRUE)[] 
[1790] [1791] [1792] [1793]
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 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1794]
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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
[1795] [1796] [1797] [1798] [1799]
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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"))[] 
[1805] [1806] [1807] [1808]
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[]\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
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es"),[] 
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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/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
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\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
[1818]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1819] [1820]
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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 ',
[1821]
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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 ',
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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
[1822] [1823] [1824]) (./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 ',
[1825] [1826] [1827]
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[]\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si
m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault
[1828]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1829]
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 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1830] [1831] [1832]
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\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
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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(),[] 
[1833]
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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-
[1834]
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 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1835]
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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
[1836]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1837]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1838]
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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
[1839] [1840]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1841]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1842] [1843] [1844] [1845] [1846]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1847] [1848]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1849]
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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1850]
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 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1851]
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1852]
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1853] [1854]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
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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")[] 
[1855]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1856]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1857]
Underfull \hbox (badness 1082) in paragraph at lines 2305--2309
[][][]\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;
[1858]
Underfull \hbox (badness 10000) in paragraph at lines 2342--2344
[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2374--2381
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1859] [1860] [1861]
Underfull \hbox (badness 10000) in paragraph at lines 2563--2565
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1862] [1863] [1864] [1865]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2854--2857
[]\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
[1866]
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 []\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 '[] 
[1867]
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[]\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
[1868] [1869] [1870] [1871] [1872] [1873] [1874]
Underfull \hbox (badness 1072) in paragraph at lines 3484--3492
[]\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
[1875]
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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[]\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
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\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
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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1876] [1877]
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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 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1878] [1879] [1880]
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[]\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
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1881]
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 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1882] [1883] [1884] [1885] [1886]
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 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1887]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4373 ...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.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [1888] [1889] [1890]
[1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901]
[1902]
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 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1903]
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[]\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
[1904]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1905] [1906] [1907]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
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\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
[1908]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
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[]\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
[1909] [1910]
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[]\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
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1911]
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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
[1912]
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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/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
[1913]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed
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\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
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[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
[1914]
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[]\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-
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\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages
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\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
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[]\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
[1915]
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[][][]\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 ,
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 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1916]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's
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[]\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
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 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1917] [1918]
Underfull \hbox (badness 4132) in paragraph at lines 6468--6470
[]\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
[1919] [1920] [1921]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6626--6626
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1922] [1923]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6769--6769
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1924]
Underfull \hbox (badness 10000) in paragraph at lines 6809--6811
[]\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
[1925] [1926]
Underfull \hbox (badness 10000) in paragraph at lines 6950--6952
[]\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 6955--6957
[]\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 class
[1927] [1928] [1929]
Underfull \hbox (badness 1859) in paragraph at lines 7178--7181
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1930]
Underfull \hbox (badness 1655) in paragraph at lines 7260--7263
[]\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
[1931]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7271--7271
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7275--7275
 []\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):[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 7283--7283
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1932]
Underfull \hbox (badness 10000) in paragraph at lines 7368--7372
[]\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1
0 is also al-lowed. If
[1933] [1934] [1935] [1936]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7632--7632
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7633--7633
 []            \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 7634--7634
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
[1937]
Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\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 7676--7678
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7684--7689
[]\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,
[1938]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7730--7730
 []          \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 7731--7731
 []                                   \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[] 
[1939] [1940]
Underfull \hbox (badness 10000) in paragraph at lines 7860--7865
[]\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 7860--7865
[][]\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 10000) in paragraph at lines 7867--7870
[]\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 7867--7870
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1941]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7983--7983
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7984--7984
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1942] [1943] [1944]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8155--8155
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1945]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[1946]
Underfull \hbox (badness 10000) in paragraph at lines 8336--8340
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8336--8340
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1947] [1948]
Underfull \hbox (badness 10000) in paragraph at lines 8451--8455
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8451--8455
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1949]
Underfull \hbox (badness 10000) in paragraph at lines 8516--8520
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8516--8520
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1950] [1951] [1952] [1953]
Underfull \hbox (badness 5203) in paragraph at lines 8847--8850
[]\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
[1954] [1955] [1956]
Underfull \hbox (badness 1776) in paragraph at lines 9073--9080
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1957]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9097--9097
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1958] [1959]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9258--9258
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1960] [1961]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9439--9439
 []\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[] 
[1962] [1963]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9525--9525
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9528--9528
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9533--9533
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1964]
Underfull \hbox (badness 1077) in paragraph at lines 9605--9608
[]\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
[1965] [1966] [1967] [1968] [1969] [1970]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10045--10045
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1971]
Underfull \hbox (badness 10000) in paragraph at lines 10132--10134
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1972] [1973]
Underfull \hbox (badness 2181) in paragraph at lines 10255--10259
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 10255--10259
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 10267--10271
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1974]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10285--10285
 []\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 10289--10289
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[1975] [1976]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10421--10421
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1977]
Underfull \hbox (badness 1917) in paragraph at lines 10544--10547
[]\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 10544--10547
\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
[1978]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 10567--10567
 []\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 '[] 
[1979]
Underfull \hbox (badness 8075) in paragraph at lines 10630--10632
[]\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
[1980]
Underfull \hbox (badness 6725) in paragraph at lines 10680--10689
\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,
Underfull \hbox (badness 6428) in paragraph at lines 10680--10689
\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 10680--10689
\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 10680--10689
\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
[1981]
Underfull \hbox (badness 3646) in paragraph at lines 10806--10808
[][][]$\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 /
[1982]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10844--10844
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[1983] [1984] [1985]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1986]
Underfull \hbox (badness 2012) in paragraph at lines 11151--11157
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use
[1987]
Underfull \hbox (badness 2096) in paragraph at lines 11164--11166
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 11167--11169
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 11174--11177
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 11178--11181
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11232--11232
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
[1988]
Underfull \hbox (badness 1009) in paragraph at lines 11250--11261
[]\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
[1989]
Underfull \hbox (badness 2846) in paragraph at lines 11337--11347
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 11476--11479
[]\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-
Underfull \hbox (badness 10000) in paragraph at lines 11476--11479
\T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 11493--11496
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1992]
Underfull \hbox (badness 2158) in paragraph at lines 11572--11575
[]\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
[1993] [1994] [1995]
Underfull \hbox (badness 3333) in paragraph at lines 11752--11754
[]\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-
[1996] [1997]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11917--11917
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
[1998]
Underfull \hbox (badness 5970) in paragraph at lines 11950--11953
[]\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 11950--11953
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11961--11970
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1999]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12005--12005
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12036--12036
 []\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 12043--12043
 []\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 12045--12045
 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
[2000] [2001] [2002]
Underfull \hbox (badness 10000) in paragraph at lines 12213--12215
[]\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
[2003] [2004]
Underfull \hbox (badness 4492) in paragraph at lines 12370--12377
[]\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
Underfull \hbox (badness 6252) in paragraph at lines 12370--12377
\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 2452) in paragraph at lines 12370--12377
\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$"\T1/ptm/m/n/10 ) and
[2005] [2006] [2007]
Underfull \hbox (badness 2020) in paragraph at lines 12532--12548
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 12532--12548
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2008]
Underfull \hbox (badness 5022) in paragraph at lines 12642--12646
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2009] [2010] [2011]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12814--12814
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2012] [2013] [2014] [2015] [2016]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13178--13178
 []             \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,
 ...),[] 
[2017]
Underfull \hbox (badness 4467) in paragraph at lines 13205--13207
[]\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 13218--13222
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 13232--13236
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 13238--13243
[]\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 13238--13243
\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 13238--13243
\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 13244--13246
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
[2018]
Underfull \hbox (badness 10000) in paragraph at lines 13295--13300
[]\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 13303--13306
[][][]\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 ,
[2019]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13357--13357
 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2020] [2021] [2022]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13548
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 13561--13561
 []\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:[]
 
[2023]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13628--13628
 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13650--13650
 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2024]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13669--13669
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
Underfull \hbox (badness 1454) in paragraph at lines 13696--13700
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[2025]
Underfull \hbox (badness 1715) in paragraph at lines 13721--13724
[]\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 13766--13768
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 13778--13782
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[2026] [2027] [2028]) [2029] [2030] (./KernSmooth-pkg.tex
Chapter 15.
[2031]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2032] [2033] [2034] [2035] [2036]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2037] [2038] [2039] [2040]) (./MASS-pkg.tex
Chapter 16.
[2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051]
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))[] 
[2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062]
[2063]
Underfull \hbox (badness 7256) in paragraph at lines 1603--1605
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2415--2415
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2075] [2076] [2077] [2078]
Underfull \hbox (badness 6559) in paragraph at lines 2693--2696
[]\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
[2079] [2080] [2081]
Underfull \hbox (badness 10000) in paragraph at lines 2863--2868
\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 8189) in paragraph at lines 2863--2868
\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 ,
Underfull \hbox (badness 3557) in paragraph at lines 2899--2907
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2899--2907
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2082] [2083]
Underfull \hbox (badness 4686) in paragraph at lines 3031--3033
[]\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
Underfull \hbox (badness 1515) in paragraph at lines 3045--3049
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2084] [2085] [2086]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
Underfull \hbox (badness 5817) in paragraph at lines 3233--3235
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2087]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098]
[2099]
Underfull \hbox (badness 1845) in paragraph at lines 4162--4164
[]\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
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2107] [2108]
Underfull \hbox (badness 10000) in paragraph at lines 4810--4813
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2109]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2110] [2111] [2112] [2113] [2114]
Underfull \hbox (badness 5681) in paragraph at lines 5288--5290
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5292--5295
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2115]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2124]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5988--5988
 []\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") 
[2125] [2126]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6130 ...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.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2127]
Underfull \hbox (badness 1783) in paragraph at lines 6248--6252
[]\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
[2128] [2129] [2130] [2131]
Underfull \vbox (badness 10000) has occurred while \output is active [2132]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2133]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2134] [2135] [2136] [2137] [2138] [2139]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073
 []\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 7090--7090
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2140]
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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 7168--7174
[]\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 ) =
[2141]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2142] [2143]
Underfull \hbox (badness 5091) in paragraph at lines 7347--7350
\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
[2144] [2145]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7477--7477
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2146]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7542--7542
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2147] [2148] [2149] [2150] [2151] [2152]
Underfull \hbox (badness 4686) in paragraph at lines 7980--7982
[]\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
Underfull \hbox (badness 1515) in paragraph at lines 7996--8000
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2153] [2154]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8099--8099
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 
Underfull \hbox (badness 1590) in paragraph at lines 8123--8127
[]\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
[2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165]
[2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9502--9502
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2175]
Underfull \hbox (badness 1158) in paragraph at lines 9629--9632
[]\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),
[2176]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9711--9711
 []\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 9713--9713
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9716--9716
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187]
[2188] [2189]) (./Matrix-pkg.tex [2190]
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
Underfull \hbox (badness 10000) in paragraph at lines 41--44
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2191]
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
[2192]
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
[2193]
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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
[2194] [2195]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2196]
Underfull \hbox (badness 5119) in paragraph at lines 508--512
[]\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 4621) in paragraph at lines 512--516
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\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 546--546
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2197] [2198]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
 []\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 662--662
 []\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 675--675
 []        \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)]),[] 
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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2199]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2200] [2201] [2202]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2203]
Underfull \hbox (badness 10000) in paragraph at lines 1022--1024
[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to
Underfull \hbox (badness 1092) in paragraph at lines 1045--1050
\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2204]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- '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.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2205pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ] [2206]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2207]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
Underfull \hbox (badness 2277) in paragraph at lines 1388--1391
[]\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
[2208]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\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
[2209]
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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[] 
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2210]
Underfull \hbox (badness 6445) in paragraph at lines 1531--1538
[]\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 3861) in paragraph at lines 1531--1538
\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
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\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 1582--1588
\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
[2211]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... 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.1623 ... 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.1624 \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.1645 \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.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2212]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\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 1710--1714
\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 1721--1724
[][][]\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
[2213]
Underfull \hbox (badness 10000) in paragraph at lines 1801--1805
[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2214]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\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
[2215] [2216] [2217]
Underfull \hbox (badness 10000) in paragraph at lines 2112--2114
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2218] [2219]
Underfull \hbox (badness 10000) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2295--2299
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2220]
Underfull \hbox (badness 4713) in paragraph at lines 2330--2332
[]\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
[2221]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2222]
Underfull \hbox (badness 10000) in paragraph at lines 2549--2553
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2549--2553
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
[2223]
Underfull \hbox (badness 2707) in paragraph at lines 2605--2609
[]\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 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n 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 ;
[2224]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\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 2677--2682
[]\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 2677--2682
[][]\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
[2225]
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[]\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 2713--2718
[][]\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
[2226]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\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 2973--2974
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
Underfull \hbox (badness 1810) in paragraph at lines 2980--2982
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\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
[2227]
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\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 3012--3016
[][][]\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
[2228] [2229]
Underfull \hbox (badness 1859) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2230]
Underfull \hbox (badness 1168) in paragraph at lines 3363--3366
[]\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
[2231] [2232]
Underfull \hbox (badness 4967) in paragraph at lines 3528--3532
[]\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
[2233]
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[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
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[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2234] [2235]
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[]\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 3725--3730
\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
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial
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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2236]
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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("dsyMatrix",    ...) \T1/ptm/m/n/10 or
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
[2237]
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[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
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\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
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[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2238]
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[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2239]
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 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
[2240]
Underfull \hbox (badness 3635) in paragraph at lines 4091--4095
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2241] [2242] [2243] [2244]
Underfull \hbox (badness 10000) in paragraph at lines 4393--4398
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2245] [2246]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4544--4544
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2247] [2248]
Underfull \hbox (badness 10000) in paragraph at lines 4699--4701
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of 
a ma-trix, or the co-er-cions
[2249] [2250]
Underfull \hbox (badness 10000) in paragraph at lines 4846--4851
[]\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 ,
[2251]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4927--4927
 []\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 4933--4933
 []  \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 4940--4940
 []  \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 '[] 
[2252] [2253]
Underfull \hbox (badness 4120) in paragraph at lines 5079--5082
[]\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
[2254]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5116--5116
 []\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 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5128--5128
 []\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[] 
[2255]
Underfull \hbox (badness 1817) in paragraph at lines 5220--5229
[]\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
Underfull \hbox (badness 5637) in paragraph at lines 5262--5264
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2256]
Underfull \hbox (badness 3138) in paragraph at lines 5288--5290
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2257]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5355--5355
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
Underfull \hbox (badness 1603) in paragraph at lines 5376--5378
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2258] [2259] [2260]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5613--5613
 []\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[] 
[2261]
Underfull \hbox (badness 10000) in paragraph at lines 5694--5697
[][][]\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 5705--5705
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2262]
Underfull \hbox (badness 1622) in paragraph at lines 5742--5747
[]\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 5742--5747
\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
[2263]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5803--5803
 []\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 5804--5804
 []          \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 5811--5811
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2264] [2265]
Underfull \hbox (badness 1062) in paragraph at lines 5940--5943
[]\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 2809) in paragraph at lines 5969--5972
[]\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
[2266]
Underfull \hbox (badness 2635) in paragraph at lines 6081--6086
[]\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 6081--6086
\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
[2267]
Underfull \hbox (badness 10000) in paragraph at lines 6089--6092
[]\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 6199--6209
\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 6199--6209
[][]\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
[2268]
Underfull \hbox (badness 1184) in paragraph at lines 6281--6284
[]\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
[2269]
Underfull \hbox (badness 10000) in paragraph at lines 6379--6382
[]\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.,
[2270]
Underfull \hbox (badness 10000) in paragraph at lines 6454--6457
[]\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.,
[2271]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6470--6470
 []\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 6509--6515
[]\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 6509--6515
[][]\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 6530--6533
[]\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
[2272]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6600--6600
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2273] [2274]
Underfull \hbox (badness 6268) in paragraph at lines 6736--6739
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2275]
Underfull \hbox (badness 5036) in paragraph at lines 6760--6764
[]\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 6760--6764
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6853 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 1348) in paragraph at lines 6933--6936
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6938--6941
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 6938--6941
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
Underfull \hbox (badness 10000) in paragraph at lines 6956--6959
Underfull \hbox (badness 7326) in paragraph at lines 6966--6968
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2277]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.7029 ...*\%}{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.7137 ...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.7237 ...tcrossprod}{matrix-products}{tcrossprod}
                                                   [2278]
Underfull \hbox (badness 1881) in paragraph at lines 7335--7341
\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
[2279pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7397 \end{Details}
                    pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7397 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7408--7411
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7408--7411
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7411--7416
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 7420--7422
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2280] [2281]
Underfull \hbox (badness 1062) in paragraph at lines 7607--7610
[]\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
[2282]
Underfull \hbox (badness 2809) in paragraph at lines 7641--7644
[]\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
[2283]
Underfull \hbox (badness 10000) in paragraph at lines 7693--7695
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2284]
Underfull \hbox (badness 1406) in paragraph at lines 7733--7737
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
Underfull \hbox (badness 1019) in paragraph at lines 7733--7737
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2285]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7831--7831
 []\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 [2286]
Underfull \hbox (badness 2635) in paragraph at lines 7896--7901
[]\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 7896--7901
\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 7904--7907
[]\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.,
[2287] [2288]
Underfull \hbox (badness 10000) in paragraph at lines 8098--8100
[]\T1/ptm/m/n/10 fast
[2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8138 \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.8138 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2290]
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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 8226--8226
 []\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 8227--8227
 []\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 8340--8350
[]\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 ,
[2291]
Underfull \hbox (badness 1184) in paragraph at lines 8411--8414
[]\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
[2292]
Underfull \hbox (badness 10000) in paragraph at lines 8501--8504
[]\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.,
[2293]
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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.,
[2294]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8593--8593
 []\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
[2295]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2296] [2297]
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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 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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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
Underfull \hbox (badness 10000) in paragraph at lines 8837--8847
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2298] [2299]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8938 \aliasA{qr}{qr-methods}{qr}
                                  
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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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![] 
[2300]
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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[] 
[2301]
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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
[2302]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 9193--9193
 []\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"[] 
[2303]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9214--9214
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 9215--9215
 []\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.9234 ... the Reciprocal Condition Number}{rcond}
                                                   [2304]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2305] [2306] [2307]
Underfull \hbox (badness 10000) in paragraph at lines 9532--9534
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
Underfull \hbox (badness 1325) in paragraph at lines 9538--9546
\T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2308] [2309]
Underfull \hbox (badness 1558) in paragraph at lines 9683--9686
[]\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
[2310]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9745--9745
 []                           \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:[] 
[2311]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9811 \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"), ...)[] 
Overfull \hbox (60.78088pt too wide) in paragraph at lines 9913--9913
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2312]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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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 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
Underfull \hbox (badness 2165) in paragraph at lines 9987--9997
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
[2313]
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10080--10080
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10084--10084
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2314]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form 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,
Underfull \hbox (badness 10000) in paragraph at lines 10141--10144
[]\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
[2315]
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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
Underfull \hbox (badness 6592) in paragraph at lines 10163--10165
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2316]
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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),[] 
[2317] [2318]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2319]
Underfull \hbox (badness 4621) in paragraph at lines 10467--10471
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2320]
Underfull \hbox (badness 10000) in paragraph at lines 10543--10546
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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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[] 
[2321]
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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)[] 
[2322]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
[2323]
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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.10806 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2324] [2325]
Underfull \hbox (badness 1430) in paragraph at lines 10936--10938
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10964--10964
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2326]
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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 11125--11131
\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 ,
[2327]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
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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
[2328]
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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 11231--11233
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2329] [2330]
Underfull \hbox (badness 3525) in paragraph at lines 11349--11353
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11356--11362
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2331]
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[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
 \T1/ptm/m/it/10 sym-met-ric
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[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
Underfull \hbox (badness 10000) in paragraph at lines 11467--11472
[]\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 1259) in paragraph at lines 11467--11472
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. 
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
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\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
[2332]
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[]\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.,
[2333] [2334]
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[]\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
[2335]
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[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2336] [2337] [2338]
Underfull \hbox (badness 7362) in paragraph at lines 11981--11983
[]\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
[2339]
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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 12020--12020
 []\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)[] 
[2340] [2341]
Underfull \hbox (badness 6910) in paragraph at lines 12270--12272
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2342] [2343] [2344]) (./boot-pkg.tex
Chapter 18.
[2345] [2346] [2347] [2348] [2349] [2350] [2351]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2352]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\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-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2353]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2354]
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\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2355]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\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 851--855
[][][]\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 ,
[2356]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\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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[2358]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\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
[2359]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\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 1082--1091
\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 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2360] [2361] [2362] [2363] [2364]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\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-
[2365] [2366] [2367] [2368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2369] [2370] [2371] [2372]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
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Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2374] [2375] [2376] [2377]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\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
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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.
[2378]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\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 2437--2438
[][][]\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 ,
[2379]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\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 2533--2537
\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
[2380] [2381] [2382] [2383] [2384]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\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 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2385] [2386] [2387]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\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 ,
[2388]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2389] [2390] [2391]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2392] [2393] [2394] [2395] [2396] [2397] [2398]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2399] [2400]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2401] [2402] [2403]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\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 4368--4372
\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
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\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 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2429]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\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
[2430]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\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
[2431] [2432] [2433] [2434]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2435] [2436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\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 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2437] [2438] [2439]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\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
[2440] [2441]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex
[2450]
Chapter 19.
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex
Chapter 20.
[2467]
Underfull \hbox (badness 3098) in paragraph at lines 133--142
[]\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-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
 is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method 
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2468]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2469]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \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 253--253
 []  \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 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2470] [2471]
Underfull \vbox (badness 10000) has occurred while \output is active [2472]
[2473]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \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 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2474]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2475]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2476]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2477] [2478]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\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 
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2479]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2481]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\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 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2482]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2483]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1150--1150
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2484]
Underfull \hbox (badness 4144) in paragraph at lines 1182--1186
[]\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
[2485]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258
 []          \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 1264--1264
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2486] [2487]
Underfull \hbox (badness 10000) in paragraph at lines 1403--1408
[]\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
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[2488]
Underfull \hbox (badness 10000) in paragraph at lines 1468--1472
[][][]\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 1492--1492
 []\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 1502--1502
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2489]
Underfull \hbox (badness 5741) in paragraph at lines 1542--1545
[]\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
[2490]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2491]
Underfull \hbox (badness 5008) in paragraph at lines 1725--1733
\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
[2492] [2493]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816
 []\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 1835--1835
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2494] [2495] [2496] [2497]
Underfull \hbox (badness 10000) in paragraph at lines 2143--2145
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 10000) in paragraph at lines 2154--2157
Underfull \hbox (badness 3179) in paragraph at lines 2168--2174
[][][]\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.
[2498] [2499] [2500]
Underfull \hbox (badness 10000) in paragraph at lines 2326--2329
[][][]\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 ,
[2501]
Underfull \hbox (badness 1292) in paragraph at lines 2394--2397
[]\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
Underfull \hbox (badness 6675) in paragraph at lines 2403--2405
[]\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 2426--2429
[][][]\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 ,
[2502] [2503] [2504] [2505]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642
 []\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 ):[] 
[2506] [2507]
Underfull \hbox (badness 1067) in paragraph at lines 2829--2834
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2508]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2509] [2510]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2511] [2512] [2513]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2514]
Underfull \hbox (badness 10000) in paragraph at lines 3255--3258
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2515]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2516] [2517] [2518]
Underfull \hbox (badness 10000) in paragraph at lines 3491--3494
[]\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
Underfull \hbox (badness 3471) in paragraph at lines 3491--3494
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2519]
Underfull \hbox (badness 10000) in paragraph at lines 3554--3559
[][][]\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 ,
[2520]
Underfull \hbox (badness 4621) in paragraph at lines 3616--3621
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3616--3621
\T1/ptm/m/n/10 which 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
Underfull \hbox (badness 6268) in paragraph at lines 3628--3631
[][][]\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 ,
[2521] [2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3816
[][][]\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 3844--3847
[][][]\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 ,
[2524]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3908--3910
[]\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
[2525] [2526] [2527] [2528]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101
 []     \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 4103--4103
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
Underfull \hbox (badness 1946) in paragraph at lines 4132--4137
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2529]
Underfull \hbox (badness 10000) in paragraph at lines 4199--4207
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2530]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241
 []\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 4250--4250
 []   \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 4252--4252
 []      \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 4255--4255
 []\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 4257--4257
 []   \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 4264--4264
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2531] [2532] [2533] [2534] [2535] [2536]
Underfull \hbox (badness 10000) in paragraph at lines 4622--4628
[]\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 4638--4640
[]\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 4651--4651
 []\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 4653--4653
 []\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)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2537]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2538]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2540]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2541] [2542] [2543]) (./foreign-pkg.tex [2544]
Chapter 22.
[2545]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2546] [2547]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\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 ,
[2548]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2549] [2550] [2551]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2552]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1
0 ,
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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\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
[2553]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\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
[2554]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
 []\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 625--625
 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2555]
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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 662--662
 []\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 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2556] [2557]
Underfull \hbox (badness 10000) in paragraph at lines 813--814
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2558] [2559]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2560]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2561] [2562]
Underfull \hbox (badness 10000) in paragraph at lines 1073--1074
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2563]
Underfull \hbox (badness 1286) in paragraph at lines 1194--1198
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2564]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\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 ,
[2565]
Underfull \hbox (badness 6725) in paragraph at lines 1293--1296
[]\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
[2566]) (./lattice-pkg.tex
Chapter 23.
[2567] [2568] [2569]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2570]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 
Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334
 []       \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"),[] 
[2571]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2572]
Underfull \hbox (badness 7631) in paragraph at lines 479--484
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2573] [2574]
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
[2575] [2576] [2577] [2578]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\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
Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2579]
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
[2580] [2581]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2582] [2583] [2584]
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 ,
[2585]
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 ,
[2586]
Underfull \vbox (badness 10000) has occurred while \output is active [2587]
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
[2588]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\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
[2589]
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
[2590] [2591] [2592]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2593]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\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
[2594] [2595] [2596]
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"),[] 
Underfull \hbox (badness 4441) in paragraph at lines 2362--2366
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2597] [2598] [2599]
Underfull \hbox (badness 4441) in paragraph at lines 2547--2554
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2600] [2601]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2602]
Underfull \hbox (badness 10000) in paragraph at lines 2761--2766
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2603]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\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
Underfull \hbox (badness 6758) in paragraph at lines 2877--2881
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\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 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2604]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\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,
Underfull \hbox (badness 2772) in paragraph at lines 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2935--2941
\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
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\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
[2605] [2606]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061
 []      \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 3062--3062
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2607]
Underfull \hbox (badness 10000) in paragraph at lines 3110--3118
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\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 3143--3150
\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
[2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2612]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2613] [2614] [2615] [2616] [2617]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2618]
Underfull \hbox (badness 10000) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2619] [2620]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\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
Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\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 4105--4109
\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
[2621]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\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 4170--4174
\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
[2622] [2623]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\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 4284--4294
\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
Underfull \hbox (badness 10000) in paragraph at lines 4284--4294
\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
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\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
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\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 4312--4314
[]\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
[2624] [2625] [2626] [2627] [2628] [2629]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2630] [2631]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\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 .
[2632] [2633]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\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
[2634] [2635] [2636] [2637] [2638] [2639]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\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
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
 []              \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],[] 
[2640]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\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 5486--5489
\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
Underfull \hbox (badness 6412) in paragraph at lines 5503--5509
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2641]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\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
[2642]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2643]
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
 []                        \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"),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2644]
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2645]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\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 5857--5864
[]\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 5857--5864
\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
[2646] [2647]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\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 ,
[2648] [2649]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2650] [2651]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\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 6273--6278
\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
[2652] [2653]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2654]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\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
[2655]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\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 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2656]
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\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
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\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2657] [2658] [2659] [2660] [2661]
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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
[2662]
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2663]
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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
[2664]
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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
[2665] [2666]
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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
[2667]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2668] [2669]
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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
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\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
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\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-
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\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
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\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the
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\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2670]
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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),[] 
[2671]
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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)[] 
[2672] [2673] [2674]
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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")[] 
[2675]
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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 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
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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
[2684] [2685]
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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, ...)[] 
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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2686]
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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
[2687]
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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
[2688]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2689] [2690]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2691] [2692]
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2693]
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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
[2694] [2695] [2696] [2697] [2698] [2699] [2700]
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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 ,
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[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2704] [2705] [2706]
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[]\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime
rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Cerebrovascular 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 ,
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\T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\
T1/ptm/m/n/10 , and
[2707]
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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2708]) (./mgcv-pkg.tex
Chapter 24.
[2709] [2710]
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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,[] 
[2711]
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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.
[2712] [2713] [2714] [2715]
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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 ,
[2716] [2717] [2718] [2719]
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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
[2720]
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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
[2721]
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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).
[2722] [2723] [2724] [2725] [2726] [2727] [2728]
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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)[] 
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 
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 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 
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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",ylim=c(0,1),[] 
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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)[] 
[2730]
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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
[2732] [2733] [2734] [2735] [2736] [2737] [2738]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2739] [2740] [2741] [2742] [2743] [2744]
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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
[2745]
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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
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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.
[2746] [2747] [2748]
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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
[2749] [2750]
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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 ,
[2751]
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[2754] [2755] [2756]
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 []            \T1/pcr/m/n/10 keepData=FALSE,scale.est="fletcher",edge.correct=
FALSE)[] 
[2757] [2758] [2759] [2760] [2761]
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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)),[] 
[2762] [2763] [2764] [2765] [2766] [2767]
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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
[2768]
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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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[2771]
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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
[2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779]
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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)+[] 
[2780] [2781]
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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, 
[2782] [2783]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
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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
[2784]
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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
[2785] [2786]
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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 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2787]
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[2789] [2790]
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2791] [2792] [2793] [2794] [2795] [2796] [2797]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5311--5311
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2798] [2799] [2800] [2801] [2802]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
[2803]
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
Underfull \hbox (badness 1142) in paragraph at lines 5658--5662
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2804] [2805] [2806]
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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[2808]
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 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
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[2813] [2814]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
[2815]
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
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[2823]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2824] [2825] [2826] [2827]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
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[2839] [2840] [2841] [2842] [2843] [2844] [2845]
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[2847]
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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 8237--8240
\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 8237--8240
\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 .
[2848]
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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 8293--8296
\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
[2849] [2850] [2851]
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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,[] 
[2852] [2853] [2854]
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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
[2855] [2856] [2857]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2858] [2859] [2860] [2861] [2862] [2863]
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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
[2866]
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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
[2867]
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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,
[2868] [2869] [2870]
Underfull \hbox (badness 1253) in paragraph at lines 9639--9641
[]\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,
[2871] [2872] [2873]
Underfull \hbox (badness 1946) in paragraph at lines 9817--9824
[]\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
Underfull \hbox (badness 2042) in paragraph at lines 9817--9824
\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 9825--9828
\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.
[2874]
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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")[] 
[2875]
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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 ,
[2876] [2877] [2878] [2879] [2880]
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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) 
[2881] [2882] [2883] [2884] [2885]
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Underfull \hbox (badness 3861) in paragraph at lines 10548--10551
[]\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, 
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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-
[2887]
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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/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
[2890] [2891]
Underfull \hbox (badness 1803) in paragraph at lines 10837--10841
\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 10849--10861
\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
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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 10866--10870
\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 ,
[2892] [2893] [2894]
Underfull \hbox (badness 6876) in paragraph at lines 11061--11067
[][][]\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
[2895]
Underfull \hbox (badness 10000) in paragraph at lines 11102--11103
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2896] [2897]
Underfull \hbox (badness 10000) in paragraph at lines 11220--11221
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2898] [2899]
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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)[] 
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 []  \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs 
over (-.5,1.5)")[] 
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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/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[2900]
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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
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\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
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 11507--11508
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2904]
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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[] 
[2905]
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\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 11736--11737
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2908] [2909] [2910] [2911]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11973--11973
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 12018--12020
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2912] [2913]
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Underfull \hbox (badness 10000) in paragraph at lines 12177--12180
[]\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 12177--12180
\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 12177--12180
\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"
[2915] [2916]
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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[] 
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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-
[2917] [2918] [2919]
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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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[2922]
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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 12647--12648
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2923] [2924] [2925] [2926]
Underfull \hbox (badness 3396) in paragraph at lines 12908--12911
[][][]\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
[2927]
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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
[2928] [2929] [2930] [2931]
Underfull \hbox (badness 10000) in paragraph at lines 13177--13180
[]\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
[2932]
Underfull \hbox (badness 10000) in paragraph at lines 13210--13214
[][][]\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 13210--13214
[][]\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 13210--13214
[][]\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 ,
[2933] [2934] [2935] [2936]
Underfull \hbox (badness 2158) in paragraph at lines 13451--13451
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2937]
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 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2938] [2939]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13660--13660
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2940] [2941] [2942]
Underfull \hbox (badness 4846) in paragraph at lines 13791--13794
[]\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
[2943] [2944] [2945] [2946] [2947]
Underfull \vbox (badness 10000) has occurred while \output is active [2948]
[2949] [2950] [2951] [2952] [2953] [2954] [2955]
Underfull \hbox (badness 10000) in paragraph at lines 14616--14624
[]\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an
 ar-ray us-ing code like
Underfull \hbox (badness 10000) in paragraph at lines 14616--14624
\T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K)
[2956] [2957] [2958] [2959] [2960]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 14888--14888
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2961] [2962] [2963] [2964] [2965]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15182--15182
 []\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 15183--15183
 []\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 15195--15195
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[2966] [2967] [2968]) (./nlme-pkg.tex
Chapter 25.
[2969]
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
[2970]
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
[2971] [2972] [2973] [2974] [2975]
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,[] 
[2976] [2977]
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 ---------------------------
---------------[] 
[2978] [2979] [2980] [2981] [2982] [2983] [2984] [2985]
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"),[] 
[2986]
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
[2987] [2988] [2989] [2990] [2991] [2992] [2993]
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 ,
[2994]
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
[2995] [2996] [2997] [2998] [2999]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\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 ,
[3000]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3001]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3002] [3003]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\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 ,
[3004]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\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 ,
[3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023]
[3024]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\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 ,
[3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035]
[3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046]
[3047] [3048]
Underfull \hbox (badness 10000) in paragraph at lines 5159--5163
[][][]\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 ,
[3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 10000) in paragraph at lines 5476--5480
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5476--5480
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[3054] [3055]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5594
[][][]\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 ,
[3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064]
Underfull \hbox (badness 2799) in paragraph at lines 6097--6103
\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
[3065]
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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 ,
[3066]
Underfull \hbox (badness 2057) in paragraph at lines 6242--6253
[][][]\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 ,
[3067]
Underfull \hbox (badness 10000) in paragraph at lines 6306--6308
[]\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 6338--6338
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3068] [3069] [3070] [3071]
Underfull \hbox (badness 7133) in paragraph at lines 6556--6560
[]\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 ,
[3072]
Underfull \hbox (badness 10000) in paragraph at lines 6655--6661
[][][]\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 6682--6682
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3073]
Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3074]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3075] [3076] [3077]
Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
[][][]\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 ,
[3078]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7040--7042
[]\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
[3079] [3080] [3081]
Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
[][][]\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 ,
[3082] [3083] [3084]
Underfull \hbox (badness 10000) in paragraph at lines 7407--7415
[]\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 7407--7415
\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 1817) in paragraph at lines 7407--7415
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7430--7433
[][][]\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 ,
[3085] [3086] [3087]
Underfull \hbox (badness 3354) in paragraph at lines 7645--7647
[]\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
[3088] [3089] [3090] [3091] [3092] [3093]
Underfull \hbox (badness 1642) in paragraph at lines 8037--8059
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3094] [3095]
Underfull \hbox (badness 10000) in paragraph at lines 8157--8174
[][][]\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 8157--8174
[][]\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 8200--8200
 []    \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
[3096] [3097] [3098] [3099] [3100]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474
 []\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
[3101]
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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.8565 \aliasA{sigma}{lmeObject}{sigma}
                                        [3102] [3103] [3104]
Underfull \hbox (badness 10000) in paragraph at lines 8726--8738
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113]
Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
[][][]\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 9328--9328
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3114]
Underfull \hbox (badness 6300) in paragraph at lines 9410--9413
[]\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
[3115] [3116] [3117] [3118]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9679 ...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.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3119]
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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
[3120] [3121] [3122]
Underfull \hbox (badness 2435) in paragraph at lines 9917--9922
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 7291) in paragraph at lines 10207--10209
[]\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
[3128] [3129] [3130]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3131]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3132] [3133] [3134]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3135] [3136]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10790--10795
[]\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[][][]
[3137]
Underfull \hbox (badness 10000) in paragraph at lines 10812--10816
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
[]\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 10867--10867
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3138] [3139] [3140] [3141]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3142] [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152]
[3153]
Underfull \hbox (badness 6268) in paragraph at lines 11902--11912
[][][]\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 ,
[3154] [3155] [3156] [3157]
Underfull \hbox (badness 10000) in paragraph at lines 12163--12169
[][][]\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 ,
[3158] [3159] [3160] [3161] [3162]
Underfull \hbox (badness 6876) in paragraph at lines 12485--12487
[]\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
[3163] [3164]
Underfull \hbox (badness 2452) in paragraph at lines 12641--12648
[][][]\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 ,
[3165]
Underfull \hbox (badness 10000) in paragraph at lines 12706--12712
[][][]\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 ,
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176]
[3177] [3178] [3179]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3180]
Underfull \hbox (badness 10000) in paragraph at lines 13685--13688
[]\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
Underfull \hbox (badness 6016) in paragraph at lines 13713--13716
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13713--13716
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13720--13723
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13728--13735
[]\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 13728--13735
\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
[3181]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
Underfull \hbox (badness 10000) in paragraph at lines 13792--13795
[]\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 13792--13795
\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
[3182]
Underfull \hbox (badness 4582) in paragraph at lines 13820--13823
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13820--13823
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13824--13827
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3183]
Underfull \hbox (badness 10000) in paragraph at lines 13900--13903
[]\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
Underfull \hbox (badness 1472) in paragraph at lines 13925--13932
\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 ,
[3184]
Underfull \hbox (badness 10000) in paragraph at lines 13994--13996
[][][]\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 ,
[3185] [3186] [3187] [3188]
Underfull \hbox (badness 1540) in paragraph at lines 14209--14214
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3189] [3190] [3191] [3192] [3193]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202]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.15153 ...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.15153 ...Extract Random Effects}{random.effects}
                                                   [3203] [3204] [3205]
[3206] [3207] [3208] [3209] [3210] [3211] [3212]
Underfull \hbox (badness 1009) in paragraph at lines 15810--15819
\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
[3213] [3214] [3215]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3216] [3217] [3218] [3219]
Underfull \hbox (badness 10000) in paragraph at lines 16235--16253
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16235--16253
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3220]
Underfull \hbox (badness 10000) in paragraph at lines 16292--16298
[][][]\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 ,
[3221]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3222] [3223] [3224] [3225] [3226] [3227] [3228]
Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3229] [3230] [3231] [3232] [3233]
Underfull \hbox (badness 1867) in paragraph at lines 17147--17156
\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 17147--17156
\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"
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3234]
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3235] [3236] [3237] [3238]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17465
[][][]\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 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 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3239] [3240] [3241] [3242] [3243] [3244] [3245] [3246]
Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
[][][]\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 17993--18003
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18031--18036
\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
[3247]
Underfull \hbox (badness 3579) in paragraph at lines 18095--18100
\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
[3248]
Underfull \hbox (badness 3579) in paragraph at lines 18158--18163
\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
[3249]
Underfull \hbox (badness 1577) in paragraph at lines 18219--18221
[]\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 18221--18226
\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
[3250]
Underfull \hbox (badness 3579) in paragraph at lines 18284--18289
\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
[3251]
Underfull \hbox (badness 10000) in paragraph at lines 18317--18326
[][][]\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 18317--18326
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18356--18361
\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
[3252] [3253] [3254]
Underfull \hbox (badness 1009) in paragraph at lines 18505--18514
\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
[3255] [3256]
Underfull \hbox (badness 1009) in paragraph at lines 18639--18648
\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
[3257] [3258] [3259] [3260] [3261] [3262] [3263] [3264]) (./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}
                                                   [3265]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3266] [3267] [3268]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3269]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\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 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3270]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3271]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3272]) (./rpart-pkg.tex
Chapter 27.
[3273] [3274] [3275] [3276]
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, ...)[] 
[3277]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3278] [3279] [3280]
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
[3281] [3282]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3283]
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[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3284]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3285]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3286] [3287] [3288]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\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, ...)[] 
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3289]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\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
[3290]
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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 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3291] [3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\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 ',
[3297] [3298]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3299] [3300] [3301]) (./spatial-pkg.tex [3302]
Chapter 28.
[3303] [3304] [3305] [3306] [3307] [3308]
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[3309] [3310] [3311] [3312] [3313] [3314] [3315] [3316] [3317] [3318] [3319]
[3320] [3321]) (./survival-pkg.tex [3322]
Chapter 29.
[3323] [3324]
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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.[] 
[3325] [3326]
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 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 
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 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.319 ... 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.319 ... Myelogenous Leukemia survival data}{aml}
                                                   [3327] [3328]
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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)[] 
[3329]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3330] [3331]
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 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3333] [3334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 798--798
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3335] [3336] [3337]
Underfull \hbox (badness 1097) in paragraph at lines 968--970
[]\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 988--988
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3338] [3339]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3340]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1171 ...erapy for Stage B/C colon cancer}{colon}
                                                  
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[3342] [3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3347] [3348] [3349] [3350] [3351]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1988--1988
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3352] [3353] [3354]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2237--2237
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3355] [3356] [3357] [3358] [3359]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2554--2554
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
Underfull \hbox (badness 1389) in paragraph at lines 2567--2569
[]\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
[3360]
Underfull \hbox (badness 1048) in paragraph at lines 2621--2623
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3361]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2698--2698
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3362] [3363] [3364] [3365]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2945--2945
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3366] [3367] [3368] [3369]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3211--3211
 []                    \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 )))[] 
[3370] [3371] [3372] [3373]
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[3375] [3376]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3620--3620
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3377] [3378]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3809--3809
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3379] [3380]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3925--3925
 []\T1/pcr/m/n/9 mresid <- (lung$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[] 
[3381]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4015--4015
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3382] [3383] [3384]
Underfull \hbox (badness 1852) in paragraph at lines 4163--4165
[]\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
[3385] [3386]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4297--4297
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4298--4298
 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3387] [3388]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4462--4462
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3389]
Underfull \hbox (badness 1540) in paragraph at lines 4517--4520
[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3390]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4585--4585
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3391] [3392]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4732--4732
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3393]
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[3395] [3396]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5029--5034
[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5029--5034
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \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/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5029--5034
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3397] [3398] [3399] [3400]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5302--5302
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 5303--5303
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3401]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5358--5358
 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3402] [3403] [3404] [3405] [3406]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5693--5693
 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5694--5694
 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3407] [3408] [3409] [3410]
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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 ),[] 
[3411] [3412] [3413] [3414]
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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
[3415]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3416]
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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
Underfull \hbox (badness 3000) in paragraph at lines 6429--6431
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3417]
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3418]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3419] [3420] [3421]
Underfull \hbox (badness 10000) in paragraph at lines 6770--6775
[][][]\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 (18.78088pt too wide) in paragraph at lines 6791--6791
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3422] [3423] [3424]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3425]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3426] [3427]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3428] [3429] [3430] [3431]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3432]
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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
[3433] [3434]
Underfull \hbox (badness 2035) in paragraph at lines 7798--7805
\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 .
Underfull \hbox (badness 10000) in paragraph at lines 7798--7805
\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 7798--7805
\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
[3435]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3436] [3437] [3438]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8032--8032
 []                 \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 )[] 
[3439] [3440]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8167--8167
 []                 \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 )[] 
[3441] [3442] [3443] [3444]
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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)[] 
[3445] [3446] [3447] [3448]
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[3450])
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Chapter 1.
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[3]
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[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one 
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[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
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^ ulp.digits \T1/ptm/m/n/10 if ei-
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\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \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,
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\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally
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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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g \T1/ptm/m/n/10 is 0; oth-er-wise, it is
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-
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\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [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]
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[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[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 ',
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ALSE) 
[16] [17] [18] [19]
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[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22] [23]
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[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
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ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
 of
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[][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 .
 See also the
[27]
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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
[28]
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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
[29] [30]
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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)[] 
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())
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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
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
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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
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
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\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
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-ited by set-ting
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ob-ject
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[64] [65]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[66] [67]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4420--4420
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
[68]
Underfull \hbox (badness 1199) in paragraph at lines 4450--4456
[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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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
[69]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
Underfull \hbox (badness 2181) in paragraph at lines 4541--4546
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[70]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[71] [72] [73] [74]
Underfull \hbox (badness 2521) in paragraph at lines 4873--4875
[]\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
[75] [76] [77] [78] [79] [80]
Underfull \hbox (badness 10000) in paragraph at lines 5270--5278
[]\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
[81] [82] [83] [84] [85] [86] [87] [88]
Underfull \hbox (badness 1796) in paragraph at lines 5830--5838
[]\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 : / /
[89] [90]
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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 6027--6027
 []\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}[] 
[91] [92] [93]
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[]\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
Underfull \hbox (badness 3009) in paragraph at lines 6197--6200
[]\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
Underfull \hbox (badness 1102) in paragraph at lines 6214--6227
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
Underfull \hbox (badness 1308) in paragraph at lines 6228--6236
[]\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
[94] [95]
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 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[96]
Overfull \hbox (107.35893pt too wide) in paragraph at lines 6423--6425
[]\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 : 
[97] [98]
Underfull \hbox (badness 10000) in paragraph at lines 6565--6568
[]\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 6565--6568
\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
[99] [100]
Underfull \hbox (badness 1248) in paragraph at lines 6747--6753
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
Underfull \hbox (badness 2080) in paragraph at lines 6747--6753
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
Underfull \hbox (badness 10000) in paragraph at lines 6767--6769
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[101]
Underfull \hbox (badness 1067) in paragraph at lines 6809--6816
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[102] [103]
Underfull \vbox (badness 10000) has occurred while \output is active [104]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7001--7001
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[105]
Underfull \hbox (badness 1231) in paragraph at lines 7126--7132
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[106] [107] [108] [109]
Underfull \hbox (badness 10000) in paragraph at lines 7337--7339
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[110] [111]
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 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
Underfull \hbox (badness 4595) in paragraph at lines 7524--7527
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[112] [113] [114]
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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)[] 
[115] [116]
Underfull \hbox (badness 8132) in paragraph at lines 7821--7825
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7821--7825
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 7840--7850
[]\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 1062) in paragraph at lines 7840--7850
[][]\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
[117]
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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")
Underfull \hbox (badness 7451) in paragraph at lines 7911--7921
[][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-
Underfull \hbox (badness 3449) in paragraph at lines 7911--7921
\T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10
 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a
m-
[118] [119] [120] [121] [122] [123]
Underfull \hbox (badness 10000) in paragraph at lines 8340--8352
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8340--8352
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[124] [125] [126]
Underfull \hbox (badness 5802) in paragraph at lines 8567--8571
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
Underfull \hbox (badness 10000) in paragraph at lines 8602--8603
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8787--8791
[]\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
[130]
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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 8877--8877
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
[131]
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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"),[] 
[132] [133]
Underfull \hbox (badness 5403) in paragraph at lines 9021--9023
[]\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 9040--9042
[]\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
[134]
Underfull \hbox (badness 1132) in paragraph at lines 9112--9119
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[135]
Underfull \hbox (badness 1603) in paragraph at lines 9248--9251
[]\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
[136] [137] [138] [139] [140] [141] [142] [143] [144]
Underfull \hbox (badness 1917) in paragraph at lines 9854--9859
[]\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
[145]
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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 9910--9910
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[146] [147]
Underfull \hbox (badness 1168) in paragraph at lines 10012--10017
\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 10051--10057
[]\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
Underfull \hbox (badness 5403) in paragraph at lines 10058--10061
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[148] [149] [150]
Underfull \hbox (badness 2828) in paragraph at lines 10217--10221
[][][]$\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 10217--10221
\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 / Double _
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10250--10250
 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[151] [152] [153] [154]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10465--10465
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[155]
Underfull \hbox (badness 1629) in paragraph at lines 10539--10543
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[156]
Underfull \hbox (badness 2150) in paragraph at lines 10640--10643
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[157]
Underfull \hbox (badness 3690) in paragraph at lines 10654--10662
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
Underfull \hbox (badness 10000) in paragraph at lines 10663--10665
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
Underfull \hbox (badness 3735) in paragraph at lines 10683--10690
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[158] [159] [160]
Underfull \hbox (badness 10000) in paragraph at lines 10879--10882
[]\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
[161] [162] [163] [164] [165] [166] [167] [168] [169]
Underfull \hbox (badness 5288) in paragraph at lines 11576--11578
[]\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 11586--11591
[]\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
[170]
Underfull \hbox (badness 10000) in paragraph at lines 11646--11648
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[171] [172]
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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
[173] [174]
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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
Underfull \hbox (badness 2790) in paragraph at lines 11921--11923
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[175] [176] [177]
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[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 12092--12102
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[178] [179] [180]
Underfull \hbox (badness 5460) in paragraph at lines 12340--12349
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
Underfull \hbox (badness 2221) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[181] [182] [183] [184] [185]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12714--12714
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[186] [187] [188] [189]
Underfull \hbox (badness 5119) in paragraph at lines 12999--13002
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[190] [191]
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\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13421--13423
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[196] [197]
Underfull \hbox (badness 10000) in paragraph at lines 13536--13538
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[198] [199]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13795--13799
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13806--13809
[][][]$\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[] 
[202]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[203]
Underfull \hbox (badness 10000) in paragraph at lines 13942--13945
[][][]\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 13952--13952
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[204]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14027--14027
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[205]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 7238) in paragraph at lines 14080--14087
[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 14080--14087
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 14080--14087
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 14088--14092
[]\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,
[206] [207] [208]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14251--14251
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14252--14252
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[209]
Underfull \hbox (badness 10000) in paragraph at lines 14331--14335
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 14331--14335
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[210] [211]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14479--14479
 []\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 14482--14482
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[212]
Underfull \hbox (badness 1168) in paragraph at lines 14566--14570
[]\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-
Underfull \hbox (badness 2012) in paragraph at lines 14566--14570
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[213]
Underfull \hbox (badness 6944) in paragraph at lines 14661--14664
[][][]\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 ,
[214]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14686--14686
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[215] [216]
Underfull \hbox (badness 10000) in paragraph at lines 14820--14822
[]\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
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14839--14839
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14841--14841
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14844--14844
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[] 
Underfull \hbox (badness 2790) in paragraph at lines 14850--14853
[]\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
[217]
Underfull \hbox (badness 4254) in paragraph at lines 14866--14874
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14881--14885
[]\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
[218]
Underfull \hbox (badness 10000) in paragraph at lines 14950--14952
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14956--14960
[]\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,
Underfull \hbox (badness 10000) in paragraph at lines 14956--14960
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 14961--14969
[]\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
Underfull \hbox (badness 3601) in paragraph at lines 14995--14999
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 14995--14999
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15062--15062
 []\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 ")[] 
[220]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15084--15084
 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[] 
[221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15902--15902
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[233]
Underfull \hbox (badness 2418) in paragraph at lines 16011--16015
\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 16018--16021
[]\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
Underfull \hbox (badness 2326) in paragraph at lines 16046--16053
[][][]\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 ,
[234] [235] [236] [237]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16292--16292
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 16317--16324
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16585--16585
 []  \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 [242]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16614--16614
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
[243]
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 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
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[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16671--16675
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[244] [245] [246] [247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17030--17030
 []\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))) 
[248] [249] [250] [251]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17284--17284
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[252] [253] [254]
Underfull \hbox (badness 2435) in paragraph at lines 17545--17547
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[255]
Underfull \hbox (badness 1867) in paragraph at lines 17587--17594
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17587--17594
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
Underfull \hbox (badness 1490) in paragraph at lines 17587--17594
\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
Underfull \hbox (badness 2285) in paragraph at lines 17602--17604
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17610--17610
 []\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.[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17620--17620
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 
[256]
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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[257] [258]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17774--17774
 []\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[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17783--17783
 []\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 17789--17789
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[259] [260]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17916--17916
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17924--17924
 []\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):[] 
[261] [262] [263]
Underfull \hbox (badness 10000) in paragraph at lines 18129--18131
[]\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
[264]
Underfull \hbox (badness 4217) in paragraph at lines 18213--18222
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18228--18244
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 4699) in paragraph at lines 18642--18645
[]\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 ,
[271] [272]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18765--18765
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[273] [274]
Underfull \hbox (badness 4739) in paragraph at lines 18900--18902
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[275] [276] [277] [278] [279] [280] [281]
Underfull \hbox (badness 1430) in paragraph at lines 19313--19318
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 19313--19318
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 19374--19379
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[283]
Underfull \hbox (badness 10000) in paragraph at lines 19434--19441
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 19434--19441
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 19434--19441
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with
Underfull \hbox (badness 5908) in paragraph at lines 19434--19441
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
Underfull \hbox (badness 10000) in paragraph at lines 19450--19452
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[284]
Underfull \hbox (badness 1975) in paragraph at lines 19522--19525
[]\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
[285] [286] [287] [288] [289] [290]
Underfull \hbox (badness 1077) in paragraph at lines 19917--19922
[]\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
[291]
Underfull \hbox (badness 10000) in paragraph at lines 19931--19938
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20005--20009
[]\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-tory
[293]
Underfull \hbox (badness 10000) in paragraph at lines 20135--20139
[]\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 20135--20139
[][]\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
[294] [295]
Underfull \hbox (badness 10000) in paragraph at lines 20233--20240
[][][]\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 ,
[296] [297]
Underfull \hbox (badness 10000) in paragraph at lines 20354--20358
[]\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
[298]
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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 20424--20429
\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 20424--20429
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20424--20429
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[299] [300]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20591--20591
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20595--20595
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[301]
Underfull \hbox (badness 3343) in paragraph at lines 20651--20655
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20737--20737
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20748--20748
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[303] [304]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20859--20859
 []\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 20862--20862
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
[305]
Underfull \hbox (badness 6380) in paragraph at lines 20907--20912
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 1960) in paragraph at lines 20965--20972
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or
Underfull \hbox (badness 1043) in paragraph at lines 20965--20972
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
[306]
Underfull \hbox (badness 2564) in paragraph at lines 20985--20988
[]\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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21015--21015
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[307]
Underfull \hbox (badness 1205) in paragraph at lines 21038--21043
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[308]
Underfull \hbox (badness 1400) in paragraph at lines 21183--21187
[][][]\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
[309]
Overfull \hbox (36.83002pt too wide) in paragraph at lines 21203--21210
[]\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo
gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ;
Underfull \hbox (badness 4886) in paragraph at lines 21203--21210
\T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m
/n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the
[310] [311]
Underfull \hbox (badness 2469) in paragraph at lines 21353--21359
[]\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. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 21353--21359
\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 names.
Underfull \hbox (badness 10000) in paragraph at lines 21353--21359
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[312] [313] [314] [315]
Underfull \hbox (badness 10000) in paragraph at lines 21670--21672
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[316] [317] [318] [319] [320]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 21974--21974
 []\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 21975--21975
 []        \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 21978--21978
 []\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)[] 
[321] [322]
Underfull \hbox (badness 1655) in paragraph at lines 22102--22106
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[323] [324] [325] [326]
Underfull \hbox (badness 2277) in paragraph at lines 22351--22354
[]\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.
[327] [328] [329] [330] [331] [332] [333]
Underfull \hbox (badness 10000) in paragraph at lines 22836--22842
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22836--22842
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[334]
Underfull \hbox (badness 1484) in paragraph at lines 22868--22876
[]\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 2951) in paragraph at lines 22868--22876
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22868--22876
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[335]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22945--22945
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[336]
Underfull \hbox (badness 10000) in paragraph at lines 22999--23003
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
Underfull \hbox (badness 10000) in paragraph at lines 22999--23003
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 10000) in paragraph at lines 23450--23458
\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 ;
[343] [344]
Underfull \hbox (badness 3849) in paragraph at lines 23564--23569
[]\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
[345]
Underfull \hbox (badness 7308) in paragraph at lines 23641--23647
[]\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 5077) in paragraph at lines 23641--23647
\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 10000) in paragraph at lines 23651--23654
[]\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 23651--23654
\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
[346] [347]
Underfull \hbox (badness 10000) in paragraph at lines 23803--23805
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[348] [349] [350]
Underfull \hbox (badness 6188) in paragraph at lines 24022--24025
[]\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
[351] [352] [353] [354] [355] [356] [357]
Underfull \hbox (badness 2197) in paragraph at lines 24494--24498
[]\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 24494--24498
\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
[358]
Underfull \hbox (badness 2846) in paragraph at lines 24508--24512
[]\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-
Underfull \hbox (badness 1990) in paragraph at lines 24508--24512
\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
[359]
Underfull \hbox (badness 10000) in paragraph at lines 24601--24607
[]\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 24601--24607
\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 24614--24616
[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 24665--24665
 [] \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:[] 
[361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24858--24864
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 24858--24864
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
Underfull \hbox (badness 10000) in paragraph at lines 24858--24864
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[364]
Underfull \hbox (badness 4120) in paragraph at lines 24944--24951
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[365] [366]
Underfull \hbox (badness 1694) in paragraph at lines 25080--25083
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[367] [368] [369]
Underfull \hbox (badness 1603) in paragraph at lines 25327--25329
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[370] [371]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 25450--25458
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[372]
Underfull \hbox (badness 5475) in paragraph at lines 25587--25597
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
[373]
Underfull \hbox (badness 3271) in paragraph at lines 25629--25632
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 25644--25646
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[374] [375] [376]
Underfull \hbox (badness 3138) in paragraph at lines 25907--25913
[]\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 25907--25913
\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 25907--25913
\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
Underfull \hbox (badness 1194) in paragraph at lines 25920--25923
[]\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 25944--25946
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 25956--25960
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25956--25960
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 25961--25967
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
[377]
Underfull \hbox (badness 3826) in paragraph at lines 25976--25981
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 25982--25993
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 25994--25997
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 26004--26016
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 1072) in paragraph at lines 26004--26016
[][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar
e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a
Underfull \hbox (badness 10000) in paragraph at lines 26018--26025
[]\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 10000) in paragraph at lines 26018--26025
\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
Underfull \hbox (badness 6380) in paragraph at lines 26018--26025
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 26018--26025
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[378] [379] [380] [381] [382]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26349--26349
 []\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 26362--26366
[]\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 26362--26366
\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)]
[383] [384] [385] [386] [387]
Underfull \hbox (badness 4341) in paragraph at lines 26686--26688
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 26722--26728
[][][]\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
[388]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26744--26744
 []\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 26756--26756
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27190--27194
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[396]
Underfull \hbox (badness 1796) in paragraph at lines 27256--27259
[]\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
[397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27453--27456
[]\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
[400] [401] [402] [403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1226) in paragraph at lines 28085--28090
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[409]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28130--28130
 []           \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))[] 
[410] [411] [412] [413]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28396--28396
 []\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 28407--28407
 []\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 28413--28413
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28414--28414
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28417--28417
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[414]
Underfull \hbox (badness 7415) in paragraph at lines 28492--28496
[]\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
[415]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28513--28513
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[416] [417]
Underfull \hbox (badness 2418) in paragraph at lines 28672--28683
[]\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
[418]
Underfull \hbox (badness 1248) in paragraph at lines 28806--28813
\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 28806--28813
\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 /
[419] [420]
Underfull \hbox (badness 1533) in paragraph at lines 28917--28920
[]\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
[421]
Underfull \hbox (badness 1337) in paragraph at lines 29014--29017
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[422]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29062--29062
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 29080--29091
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 29092--29095
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[423] [424]
Underfull \hbox (badness 1117) in paragraph at lines 29187--29193
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[425] [426] [427] [428] [429] [430]
Underfull \hbox (badness 4048) in paragraph at lines 29565--29570
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
Underfull \hbox (badness 4582) in paragraph at lines 29565--29570
\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 29565--29570
\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 ,
[431] [432] [433] [434] [435] [436] [437] [438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30111--30111
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[439] [440] [441] [442]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 30397--30399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[443] [444] [445]
Underfull \hbox (badness 7558) in paragraph at lines 30613--30617
[]\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 30623--30625
[]\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 5417) in paragraph at lines 30628--30631
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 30632--30634
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 30635--30637
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 10000) in paragraph at lines 31040--31044
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[452] [453] [454] [455] [456]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31371--31371
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31374--31374
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[457] [458] [459]
Underfull \hbox (badness 3375) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/
ptm/m/n/10 , are in-valid, e.g., du-
Underfull \hbox (badness 2359) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is 
back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal
Underfull \hbox (badness 2582) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m
atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call
[460] [461] [462]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 31755--31755
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[463] [464]
Underfull \hbox (badness 10000) in paragraph at lines 31886--31890
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 31886--31890
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[465] [466] [467]
Underfull \hbox (badness 2302) in paragraph at lines 32137--32144
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[468]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32189--32189
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[469]
Underfull \hbox (badness 1158) in paragraph at lines 32293--32298
[]\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
[470]
Underfull \hbox (badness 10000) in paragraph at lines 32320--32326
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 32320--32326
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[471]
Underfull \hbox (badness 10000) in paragraph at lines 32396--32401
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 32396--32401
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[472]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32478--32478
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[473] [474] [475]
Underfull \hbox (badness 2809) in paragraph at lines 32742--32748
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 32749--32752
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487]
Underfull \hbox (badness 1735) in paragraph at lines 33554--33560
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[488]
Underfull \hbox (badness 4303) in paragraph at lines 33570--33573
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[489] [490] [491] [492]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 33888--33888
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[493] [494] [495] [496]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34140--34140
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34142--34142
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[497]
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
[][][]\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
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
\T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T
1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
\T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i
s the de-fault cur-rently;
Underfull \hbox (badness 2512) in paragraph at lines 34200--34202
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[498]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34296--34296
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[499] [500] [501]
Underfull \vbox (badness 10000) has occurred while \output is active [502]
[503]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34624--34624
 []\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 34639--34639
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[504] [505] [506] [507] [508] [509]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35078--35078
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35079--35079
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[510] [511] [512] [513]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35343--35343
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[514]
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
[]\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 '
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 35427--35437
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
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\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
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\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[515]
Underfull \hbox (badness 10000) in paragraph at lines 35471--35477
[]\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 35471--35477
\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 35471--35477
\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 1728) in paragraph at lines 35483--35490
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 35483--35490
\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 35483--35490
\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
[516] [517] [518] [519] [520]
Underfull \hbox (badness 10000) in paragraph at lines 35824--35830
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[521] [522] [523]
Underfull \hbox (badness 1163) in paragraph at lines 36012--36019
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 36012--36019
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[524] [525] [526] [527]
Underfull \hbox (badness 1142) in paragraph at lines 36275--36281
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36290--36290
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[528] [529] [530]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36538--36538
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[531]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36582--36582
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[532] [533] [534] [535] [536] [537] [538]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37016--37016
 []\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 37019--37019
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[539]
Underfull \hbox (badness 10000) in paragraph at lines 37070--37077
[]\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 37070--37077
\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 ).
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37121--37121
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[540] [541] [542] [543]
Underfull \hbox (badness 2762) in paragraph at lines 37360--37369
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 37360--37369
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple
[544]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 37422--37422
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[545] [546]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37587--37587
 []\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. 
[547]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 37625--37625
 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
[548]
Underfull \hbox (badness 3219) in paragraph at lines 37674--37679
[]\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 37674--37679
\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
[549]
Underfull \hbox (badness 2452) in paragraph at lines 37764--37767
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 37764--37767
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 37951--37955
[]\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
Underfull \hbox (badness 1584) in paragraph at lines 37966--37969
[]\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
[553] [554]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38098--38098
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38168--38168
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[556] [557] [558]
Underfull \hbox (badness 1082) in paragraph at lines 38306--38309
[]\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
[559] [560]
Underfull \hbox (badness 1038) in paragraph at lines 38493--38496
[]\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
[561] [562] [563] [564] [565] [566]
Underfull \hbox (badness 1515) in paragraph at lines 38857--38860
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[567] [568] [569]
Underfull \hbox (badness 4096) in paragraph at lines 39098--39101
[]\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 ,
[570] [571]
Underfull \hbox (badness 10000) in paragraph at lines 39212--39216
[]\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.,
[572] [573]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 39365--39365
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 39367--39367
 []            \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 39369--39369
 []                 \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[] 
[574]
Underfull \hbox (badness 10000) in paragraph at lines 39382--39384
[]\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
[575]
Underfull \hbox (badness 10000) in paragraph at lines 39462--39465
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[576] [577]
Underfull \hbox (badness 1867) in paragraph at lines 39580--39584
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 39642--39646
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[578] [579] [580] [581] [582] [583] [584]
Underfull \hbox (badness 10000) in paragraph at lines 40060--40067
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40116--40125
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40116--40125
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40126--40134
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40126--40134
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 1303) in paragraph at lines 40126--40134
\T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by
 de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[585]
Underfull \hbox (badness 1337) in paragraph at lines 40192--40200
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40201--40204
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[586]
Underfull \hbox (badness 4429) in paragraph at lines 40258--40260
[][][]$\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 40267--40267
 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[587] [588] [589]
Underfull \hbox (badness 10000) in paragraph at lines 40484--40486
[]\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
[590] [591]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40606--40606
 []\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 40608--40608
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [592]
[593] [594] [595] [596]
Underfull \hbox (badness 6542) in paragraph at lines 40970--40972
[]\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
[597] [598] [599]
Underfull \hbox (badness 3460) in paragraph at lines 41136--41139
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via
Underfull \hbox (badness 1708) in paragraph at lines 41143--41151
[]\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 41143--41151
\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
Underfull \hbox (badness 10000) in paragraph at lines 41152--41156
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 41152--41156
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 41152--41156
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 41173--41178
[][][]\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;
[600]
Underfull \hbox (badness 3895) in paragraph at lines 41235--41247
[]\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 41235--41247
\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 ,
[601] [602] [603]
Underfull \hbox (badness 10000) in paragraph at lines 41420--41423
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[604] [605]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 41557--41557
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[606] [607] [608] [609] [610] [611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42024--42024
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 42033--42033
 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[613]
Underfull \hbox (badness 1803) in paragraph at lines 42150--42153
[]\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 2334) in paragraph at lines 42154--42161
[]\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
[614]
Underfull \hbox (badness 4726) in paragraph at lines 42180--42184
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
Underfull \hbox (badness 1122) in paragraph at lines 42180--42184
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[615] [616]
Underfull \hbox (badness 3668) in paragraph at lines 42369--42371
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[617] [618]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 42473--42473
 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[619]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42548--42548
 []\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[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 42556--42556
 []\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 ...[] 
[620] [621]
Underfull \hbox (badness 6220) in paragraph at lines 42686--42691
[]\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 42686--42691
\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 1533) in paragraph at lines 42686--42691
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
Underfull \hbox (badness 6592) in paragraph at lines 42702--42707
[]\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
[622]
Underfull \hbox (badness 1603) in paragraph at lines 42721--42725
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[623]
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[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
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\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
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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
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[624] [625]
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[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[626] [627] [628] [629]
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[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
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\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[630]
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[]\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
[631]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
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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
[632]) (./compiler-pkg.tex
Chapter 2.
[633]
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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
[634] [635] [636]) (./datasets-pkg.tex
Chapter 3.
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[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[637] [638] [639] [640] [641]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[642]
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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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[644] [645] [646] [647]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[648] [649]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[650] [651]
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[]\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.
[652] [653]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[654] [655] [656] [657] [658]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[659] [660]
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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
[661] [662] [663]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[664]
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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)[] 
[665] [666]
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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]]))))[] 
[667] [668] [669] [670]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[671] [672] [673] [674] [675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[679]
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[680]
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[682]
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[683] [684]
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[685]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[686] [687] [688] [689] [690] [691] [692]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[693] [694]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[695]
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[696]
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\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
 datasets .
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[697]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
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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 /
[698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709]
[710] [711]) (./grDevices-pkg.tex [712]
Chapter 4.
[713] [714] [715] [716] [717] [718]
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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/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[719]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[720] [721] [722] [723] [724] [725] [726] [727] [728]
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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
[729]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[730]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
[731]
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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[732]
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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
[733] [734] [735]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[736]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
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[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[737] [738] [739]
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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
[740]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
[741]
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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 ,
[742]
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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
[743] [744]
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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
[745] [746]
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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
[747] [748]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
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[750] [751] [752] [753] [754]
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[756] [757] [758] [759] [760]
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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))[] 
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[761]
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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
[762] [763] [764]
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 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[765]
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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
[766]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[767] [768] [769] [770]
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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 ,
[771] [772] [773] [774] [775]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[776]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[778]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[779] [780]
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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
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[781]
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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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[782]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[783]
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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
[784] [785]
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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
[786] [787]
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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
[788]
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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
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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 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[789] [790]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[791]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[792] [793]
Underfull \hbox (badness 10000) in paragraph at lines 5401--5403
[]\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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[794] [795] [796] [797] [798]
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 []\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 5772--5775
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[799] [800] [801] [802] [803] [804] [805]
Underfull \hbox (badness 1189) in paragraph at lines 6169--6171
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[806]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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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
[807]
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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
[808]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[809]
Underfull \hbox (badness 10000) in paragraph at lines 6467--6470
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[810]
Underfull \hbox (badness 5637) in paragraph at lines 6558--6564
\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 /
[811] [812] [813]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via
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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
[814] [815] [816]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 10000) 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
[817] [818] [819] [820]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[821] [822] [823]
Underfull \hbox (badness 2726) in paragraph at lines 466--472
[]\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
[824] [825] [826]
Underfull \hbox (badness 10000) in paragraph at lines 659--663
[]\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
Underfull \hbox (badness 2735) in paragraph at lines 687--694
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[827]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[828] [829]
Underfull \hbox (badness 1062) in paragraph at lines 853--856
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[830] [831] [832] [833] [834] [835] [836]
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 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 
[837]
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\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 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, 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 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[838]
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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)[] 
[839] [840] [841] [842] [843]
Underfull \hbox (badness 10000) in paragraph at lines 1747--1753
[][][]\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
[844]
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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 = "")[] 
[845]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[846] [847]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, 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))[] 
[848] [849] [850] [851] [852]
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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
[853] [854] [855] [856] [857]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[858] [859]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[860]
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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 :[] 
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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
[861]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[862] [863] [864]
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 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
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 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[865]
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[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[866]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[867] [868] [869]
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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"),[] 
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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[870] [871] [872]
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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])[] 
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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 [873]
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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")[] 
Underfull \vbox (badness 10000) has occurred while \output is active [874]
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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
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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
[875] [876]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[877]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[878] [879]
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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
[880] [881] [882] [883]
Underfull \hbox (badness 1924) in paragraph at lines 4400--4405
[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[884]
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\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
[885]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 
[886]
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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))[] 
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[887]
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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 ,
[888] [889]
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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.
[890] [891]
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<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"mai.pdf, id=2932
2, 289.08pt x 289.08pt>
<use "/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"mai.pdf>
[892 </builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/mai.pdf>]
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<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"oma.pdf, id=2933
6, 259.97125pt x 332.24126pt>
<use "/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"oma.pdf>
[893 </builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/oma.pdf>]
[894]
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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
[895]
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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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[897]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[898] [899] [900] [901]
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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)[] 
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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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[902] [903] [904] [905] [906] [907] [908]
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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[] 
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[915] [916]
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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
<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"pch.pdf, id=2974
6, 361.35pt x 50.1875pt>
<use "/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"pch.pdf>
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[][] 
[917 </builddir/build/BUILD/R-3.5.0/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,[] 
[918]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[920]
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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)))))[] 
[921]
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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
[922] [923] [924]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[925]
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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))[] 
[926] [927] [928] [929] [930] [931]
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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):[] 
[932]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[933] [934] [935] [936] [937]
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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,[] 
[938]
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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[939] [940]
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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, ...)[] 
[941] [942]
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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
[943] [944]
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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),[] 
[945] [946]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[947] [948]
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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�...")[] 
[949]
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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
[950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8789 \HeaderA{units}{Graphical Units}{units}
                                               [951]
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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
[952] [953]
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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)[] 
[954]) (./grid-pkg.tex
Chapter 6.
[955] [956] [957] [958] [959] [960]
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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/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 
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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-
[972] [973] [974]
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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
[975] [976] [977] [978] [979] [980] [981]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[982] [983] [984]
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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")[] 
[985]
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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 ,
[986]
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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
[987] [988] [989]
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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
[990] [991] [992]
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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-
[993] [994] [995]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 
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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[996] [997] [998] [999]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1000] [1001] [1002] [1003] [1004]
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1005]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[1006]
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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
[1007] [1008]
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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,[] 
[1009] [1010] [1011]
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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")[] 
[1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022]
[1023] [1024]
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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
[1025]
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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-
[1026] [1027] [1028]
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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
[1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037]
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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
[1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047]
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\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1048] [1049] [1050] [1051] [1052]
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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
[1053]
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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 ,
[1054] [1055]
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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
[1056] [1057] [1058]
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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"))))[] 
[1059]) (./methods-pkg.tex [1060]
Chapter 7.
[1061] [1062]
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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
[1063] [1064] [1065]
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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-
[1066] [1067]
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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[] 
[1068]
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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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[1071]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
 Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] 
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
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\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082]
[1083] [1084]
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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/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1085] [1086]
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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
[1087] [1088] [1089]
Underfull \hbox (badness 1132) in paragraph at lines 2214--2219
[]\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 =
[1090] [1091]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1092] [1093] [1094]
Underfull \hbox (badness 3792) in paragraph at lines 2574--2577
[]\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
[1095]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1096] [1097] [1098]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1099] [1100] [1101] [1102] [1103] [1104] [1105]
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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
[1106] [1107]
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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
[1108]
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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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[]
[1109] [1110]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
[1111]
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[]\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = 
"Pos") 
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
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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
[1112] [1113] [1114]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1115] [1116]
Underfull \hbox (badness 1629) in paragraph at lines 4247--4256
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1117]
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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,[] 
[1118]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1119] [1120]
Underfull \hbox (badness 1033) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1121]
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 ,
[1122] [1123] [1124]
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
[1125] [1126] [1127] [1128]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1129]
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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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[1131]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1132]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1133]
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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
[1134] [1135] [1136]
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
[1137]
Underfull \hbox (badness 10000) in paragraph at lines 5757--5761
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5757--5761
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1138]
Underfull \hbox (badness 10000) in paragraph at lines 5848--5852
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 10000) in paragraph at lines 6210--6226
[]\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
[1143] [1144]
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
[1145]
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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
[1146]
Underfull \hbox (badness 1072) in paragraph at lines 6575--6582
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1147]
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[]\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
[1148]
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[1150] [1151]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}
                               [1152]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
Underfull \hbox (badness 2042) in paragraph at lines 7065--7072
\T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the 
S4 bit of the ob-ject. With
[1153] [1154]
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 []\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")[] 
[1155]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
[1156]
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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 ,
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\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 ,
[1157] [1158]
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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
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[]\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
[1159] [1160]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171]
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
[1172]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1173]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1174] [1175] [1176] [1177]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1178] [1179] [1180]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1181] [1182]
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 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1184] [1185] [1186] [1187]
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 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1188]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1189]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198]
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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.,
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
[1199] [1200] [1201] [1202]) (./parallel-pkg.tex
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
[1203]
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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
[1204] [1205]
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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
[1206]
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[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1207] [1208]
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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
[1209] [1210] [1211] [1212]
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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
[1213] [1214]
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 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1215]
Underfull \hbox (badness 10000) in paragraph at lines 884--887
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1216]
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 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
[1217]
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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1218]
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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
Underfull \hbox (badness 10000) in paragraph at lines 1143--1151
[]\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
[1219]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180
 []\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)[] 
[1220] [1221]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296
 []                 \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 1310--1310
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
Underfull \hbox (badness 1577) in paragraph at lines 1339--1342
[]\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
[1222]
Underfull \hbox (badness 3375) in paragraph at lines 1385--1387
[]\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
[1223] [1224]) (./splines-pkg.tex
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
[1225] [1226] [1227] [1228] [1229] [1230] [1231]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1232] [1233] [1234] [1235]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1236] [1237] [1238]) (./stats-pkg.tex
Chapter 10.
[1239]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\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 ,
[1240] [1241] [1242] [1243] [1244]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1245] [1246] [1247] [1248] [1249] [1250] [1251]
Underfull \hbox (badness 1024) in paragraph at lines 847--849
[]\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
[1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 1391--1393
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1260]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1261] [1262] [1263] [1264]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via
Underfull \hbox (badness 2197) in paragraph at lines 1773--1777
\T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-
[1265] [1266]
Underfull \hbox (badness 4303) in paragraph at lines 1874--1876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues,
 see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/
pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with
[1267] [1268] [1269]
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2096--2101
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2102--2108
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
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\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1270] [1271]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1272] [1273] [1274]
Underfull \hbox (badness 1221) in paragraph at lines 2457--2462
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2457--2462
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1275]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1276] [1277]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1278] [1279] [1280] [1281]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1282] [1283] [1284]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 
[1285]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176
 []\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 3177--3177
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1286]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1287] [1288] [1289] [1290] [1291]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1292] [1293] [1294] [1295]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1296] [1297] [1298] [1299] [1300]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135
 []\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 4136--4136
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1301] [1302] [1303]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1304] [1305] [1306]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1307]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\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 =
[1308] [1309]
Underfull \hbox (badness 2080) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
Underfull \hbox (badness 2050) in paragraph at lines 4757--4763
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex-
ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me
th-ods, and \T1/pcr/m/n/10 coef
Underfull \hbox (badness 4954) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes
 should typ-i-cally also keep the \T1/pcr/m/n/10 complete = *
Underfull \hbox (badness 4726) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe
f(obj, complete = TF))\T1/ptm/m/n/10 ,
[1310] [1311] [1312] [1313]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019
 []\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 5021--5021
 []\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))[] 
[1314]
Underfull \hbox (badness 7397) in paragraph at lines 5108--5112
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5108--5112
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1315] [1316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242
 []\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 5260--5260
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
Underfull \hbox (badness 2680) in paragraph at lines 5287--5289
[]\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
[1317]
Underfull \hbox (badness 10000) in paragraph at lines 5292--5294
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1318] [1319]
Underfull \hbox (badness 1436) in paragraph at lines 5470--5475
[]\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 5470--5475
\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 5470--5475
\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 ,
[1320] [1321] [1322]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5669--5669
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1323]
Underfull \hbox (badness 1168) in paragraph at lines 5741--5746
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1324] [1325]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5836--5836
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1326] [1327] [1328]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6021--6021
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1329] [1330]
Underfull \hbox (badness 10000) in paragraph at lines 6184--6189
[]\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
[1331] [1332] [1333]
Underfull \hbox (badness 5954) in paragraph at lines 6380--6382
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1334]
Underfull \hbox (badness 2503) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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 6469--6474
\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,
[1335]
Underfull \hbox (badness 7238) in paragraph at lines 6505--6508
[][][]\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
[1336]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6540--6540
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6555--6555
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6570--6570
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1337] [1338] [1339] [1340]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6814--6814
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1341] [1342]
Underfull \vbox (badness 10000) has occurred while \output is active [1343]
[1344] [1345] [1346]
Underfull \hbox (badness 10000) in paragraph at lines 7212--7216
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1347]
Underfull \hbox (badness 6493) in paragraph at lines 7311--7314
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1348] [1349]
Underfull \hbox (badness 10000) in paragraph at lines 7448--7451
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1350] [1351] [1352] [1353] [1354] [1355]
Underfull \hbox (badness 10000) in paragraph at lines 7858--7863
[]\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 , ...,
[1356] [1357]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7996--7998
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1358] [1359] [1360]
Underfull \hbox (badness 1210) in paragraph at lines 8213--8215
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8664--8664
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8686--8686
 []\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 8689--8689
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1368] [1369]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8827--8827
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1370]
Underfull \hbox (badness 1859) in paragraph at lines 8866--8871
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1371] [1372] [1373]
Underfull \hbox (badness 2865) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-
Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1374] [1375]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9254--9254
 []           \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 9255--9255
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1376] [1377] [1378]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9434--9436
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1379] [1380] [1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 2443) in paragraph at lines 9887--9893
[][][]\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);
[1386] [1387] [1388]
Underfull \hbox (badness 3758) in paragraph at lines 10100--10103
[]\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
[1389] [1390] [1391] [1392]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10336--10336
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1393]
Underfull \hbox (badness 4132) in paragraph at lines 10401--10405
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1394]
Underfull \hbox (badness 10000) in paragraph at lines 10506--10509
[]\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
[1395] [1396] [1397]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\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 ^^@
[1398]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1399]
Underfull \hbox (badness 10000) in paragraph at lines 10833--10839
[][][]\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 10871--10876
\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 (=
[1400] [1401]
Underfull \hbox (badness 2635) in paragraph at lines 11004--11007
\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
[1402] [1403] [1404]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 11208--11217
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 11208--11217
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1405]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11290--11290
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1406]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11323--11323
 []            \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 11336--11340
[]\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
[1407] [1408] [1409]
Underfull \hbox (badness 7379) in paragraph at lines 11516--11519
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1410] [1411]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11655--11655
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1412]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11723--11723
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11735--11735
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
[1413]
Underfull \hbox (badness 1062) in paragraph at lines 11784--11789
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11801--11803
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1414] [1415]
Underfull \hbox (badness 3623) in paragraph at lines 11955--11957
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1416] [1417]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12051--12051
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1418]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12144--12144
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 12192--12195
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1420] [1421] [1422]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12394--12396
[]\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
[1423]
Underfull \hbox (badness 4739) in paragraph at lines 12417--12419
[]\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
[1424]
Underfull \hbox (badness 2753) in paragraph at lines 12486--12488
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1425] [1426]
Underfull \hbox (badness 1292) in paragraph at lines 12611--12615
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1427]
Underfull \hbox (badness 10000) in paragraph at lines 12724--12726
[]\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
Underfull \hbox (badness 2894) in paragraph at lines 12730--12734
[]\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 12730--12734
\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
[1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13437--13437
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1439]
Underfull \hbox (badness 4518) in paragraph at lines 13480--13485
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1440] [1441]
Underfull \hbox (badness 10000) in paragraph at lines 13679--13683
[]\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
 ,
[1442] [1443] [1444]
Underfull \hbox (badness 6995) in paragraph at lines 13864--13866
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1445] [1446]
Underfull \hbox (badness 1163) in paragraph at lines 14012--14020
\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 ,
[1447] [1448]
Underfull \hbox (badness 4518) in paragraph at lines 14132--14137
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1449] [1450]
Underfull \hbox (badness 10000) in paragraph at lines 14270--14274
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 14270--14274
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1451]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14318--14318
 []\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 14319--14319
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1452]
Underfull \hbox (badness 10000) in paragraph at lines 14374--14377
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14374--14377
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1453] [1454] [1455] [1456]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14662--14662
 []\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 14663--14663
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1457]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14713--14715
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14756--14756
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 2726) in paragraph at lines 15163--15166
[]\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 ,
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15878--15878
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1476] [1477]
Underfull \hbox (badness 1014) in paragraph at lines 16016--16021
\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
[1478]
Underfull \hbox (badness 1648) in paragraph at lines 16082--16084
[]\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 16096--16105
\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 16096--16105
\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
[1479]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16164--16164
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16718--16718
 []\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[] 
[1489] [1490] [1491]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16946--16946
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Underfull \hbox (badness 2359) in paragraph at lines 17507--17509
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1501]
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Underfull \vbox (badness 10000) has occurred while \output is active [1503]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17679--17679
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1504]
Underfull \hbox (badness 10000) in paragraph at lines 17759--17763
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1505]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17839--17839
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17886--17886
 []\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 17933--17933
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514]
Underfull \hbox (badness 1248) in paragraph at lines 18424--18427
[]\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 1127) in paragraph at lines 18437--18441
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1515]
Underfull \hbox (badness 1478) in paragraph at lines 18445--18449
\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
Underfull \hbox (badness 2042) in paragraph at lines 18503--18505
[]\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
[1516] [1517]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18609--18609
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18651--18651
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18669--18669
 []\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 18672--18672
 []\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 18692--18692
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
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 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1519]
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[]\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 18730--18741
\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
[1520]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18793--18793
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1521] [1522] [1523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19018--19018
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1524]
Underfull \hbox (badness 1337) in paragraph at lines 19094--19097
[]\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
[1525] [1526] [1527] [1528] [1529] [1530]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19413--19413
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1531]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19501--19501
 []       \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 (6.78088pt too wide) in paragraph at lines 19504--19504
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1532]
Underfull \hbox (badness 3049) in paragraph at lines 19583--19587
[]\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
[1533] [1534] [1535] [1536]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19831--19831
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 4779) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19841--19844
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1537]
Underfull \hbox (badness 1107) in paragraph at lines 19899--19901
[]\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
[1538]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19954--19954
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1539]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19961--19961
 []\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)[] 
Underfull \hbox (badness 10000) in paragraph at lines 20011--20014
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 20011--20014
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1540]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20055--20055
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1541] [1542]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20180--20180
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1543]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20245
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1544]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20291--20291
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
Underfull \hbox (badness 10000) in paragraph at lines 20346--20348
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1545]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20383--20383
 [] \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 20388--20388
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556]
[1557] [1558]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21238--21238
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1559]
Underfull \hbox (badness 6859) in paragraph at lines 21305--21312
[][][]\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 21316--21322
[]\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 ,
[1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570]
[1571]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22054--22054
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1572] [1573] [1574] [1575] [1576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22338--22338
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 22339--22339
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1577] [1578] [1579] [1580] [1581]
Underfull \hbox (badness 1337) in paragraph at lines 22662--22668
[]\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
[1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23214--23214
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1590] [1591]
Underfull \hbox (badness 1028) in paragraph at lines 23355--23358
[]\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
[1592] [1593]
Underfull \hbox (badness 10000) in paragraph at lines 23465--23468
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
Underfull \hbox (badness 5091) in paragraph at lines 23465--23468
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
Underfull \hbox (badness 10000) in paragraph at lines 23520--23522
[]\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
[1594]
Underfull \hbox (badness 10000) in paragraph at lines 23582--23584
[]\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
[1595] [1596]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23684--23684
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1597] [1598] [1599]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23904--23904
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1600] [1601] [1602]
Underfull \hbox (badness 10000) in paragraph at lines 24050--24053
[]\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
Underfull \hbox (badness 2134) in paragraph at lines 24102--24106
[][][]\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
[1603]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24115--24115
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1604] [1605] [1606] [1607] [1608] [1609] [1610]
Underfull \hbox (badness 6268) in paragraph at lines 24581--24586
[][]\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 ,
[1611]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24609--24609
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1612] [1613]
Underfull \hbox (badness 1867) in paragraph at lines 24786--24788
[]\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 24799--24803
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 24799--24803
\T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1614]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 24835--24835
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1615] [1616] [1617]
Underfull \hbox (badness 2495) in paragraph at lines 25025--25034
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1618]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25107--25107
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
Underfull \hbox (badness 1412) in paragraph at lines 25114--25116
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1619]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25201--25201
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
[1620]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 25226--25226
 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
Overfull \hbox (66.78088pt too wide) in paragraph at lines 25229--25229
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1621]
Underfull \hbox (badness 10000) in paragraph at lines 25271--25276
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 25271--25276
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1622]
Underfull \hbox (badness 2980) in paragraph at lines 25416--25418
[]\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g
iven, un-less it has been given as
[1623]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25452--25452
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25501--25501
 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
[1624]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 25522--25522
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1625]
[1626]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25626--25626
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1627]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25693--25693
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1628] [1629] [1630] [1631] [1632] [1633]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26072--26072
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
Underfull \hbox (badness 6477) in paragraph at lines 26126--26129
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1634] [1635]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 26257--26257
 []\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 26258--26258
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1636]
Underfull \hbox (badness 2922) in paragraph at lines 26327--26332
[]\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
[1637]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26364--26364
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26367--26367
 []                    \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 26376--26376
 []         \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 26377--26377
 []  \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 26381--26381
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1638]
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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
Underfull \hbox (badness 3240) in paragraph at lines 26435--26438
[][][]\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 26456--26456
 []  \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 26459--26459
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1639]
Underfull \hbox (badness 2922) in paragraph at lines 26509--26514
[]\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
[1640]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26542--26542
 []  \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 26546--26546
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26556--26556
 []  \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 26561--26561
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1641]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26619--26619
 []\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 26635--26635
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1642] [1643]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26749--26749
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1644]
Underfull \hbox (badness 2922) in paragraph at lines 26811--26816
[]\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
[1645]
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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")))[] 
[1646]
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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 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
[1647]
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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 ## 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")))[] 
[1648]
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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
[1649]
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 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
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 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1650]
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[]\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
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 []\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)[] 
[1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1659] [1660] [1661] [1662] [1663] [1664] [1665]
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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
[1666] [1667] [1668]
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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
[1669] [1670]
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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
[1671]
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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
[1672]
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 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1673] [1674]
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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)
[1675] [1676]
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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
[1677] [1678]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1679] [1680]
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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,[] 
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 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1681]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1682]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1683]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1684]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1685]
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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
[1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693]
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 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1694]
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1695] [1696] [1697] [1698]
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[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 
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 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1699] [1700]
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 []\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:[] 
[1701] [1702] [1703] [1704]
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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
[1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712]
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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
[1713]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1714] [1715] [1716] [1717] [1718]
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 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1719]
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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
[1720]
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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 "")[] 
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 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1721]) (./stats4-pkg.tex [1722]
Chapter 11.
[1723] [1724] [1725]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1726] [1727] [1728]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
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                   \relax 
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                                                   [1729]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1730] [1731]) (./tcltk-pkg.tex [1732]
Chapter 12.
[1733] [1734] [1735] [1736]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1737] [1738] [1739]
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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
[1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751]
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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
[1752]) (./tools-pkg.tex
Chapter 13.
[1753]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1754]
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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
[1755]
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 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1756]
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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 ,
[1757]
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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
[1758] [1759] [1760] [1761] [1762] [1763] [1764]
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[1765] [1766]
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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")[] 
[1767] [1768]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1769]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1770]
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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
[1771]
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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
[1772] [1773]
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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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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1774] [1775] [1776] [1777] [1778]
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 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
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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 .
[1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier
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[1785]
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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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 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1786]
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 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
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
[1787]
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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
[1788]
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
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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 .
[1789]
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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/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2423--2423
 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1790] [1791] [1792] [1793]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2688--2688
 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1794]
Underfull \hbox (badness 2486) in paragraph at lines 2733--2741
[]\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
[1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 1072) in paragraph at lines 3111--3113
[]\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
[1800] [1801] [1802] [1803] [1804]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3447--3447
 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1805] [1806] [1807] [1808]
Underfull \hbox (badness 4108) in paragraph at lines 3691--3698
[]\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
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 3791--3791
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
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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
[1811] [1812]
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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
[1813]
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 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
[1814]
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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
[1815] [1816] [1817]
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 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
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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
[1818]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1819] [1820]
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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 ',
[1821]
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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 4521--4527
[]\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 ',
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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
[1822] [1823] [1824]) (./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 ',
[1825] [1826] [1827]
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[]\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si
m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault
[1828]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1829]
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 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1830] [1831] [1832]
Underfull \hbox (badness 1946) in paragraph at lines 527--531
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
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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(),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 584--584
 []                       \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(),[] 
[1833]
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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 ,
Underfull \hbox (badness 4416) in paragraph at lines 620--626
\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-
[1834]
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 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1835]
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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
[1836]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1837]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1838]
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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
[1839] [1840]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1841]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1842] [1843] [1844] [1845] [1846]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1847] [1848]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1849]
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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1850]
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 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1851]
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1852]
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1853] [1854]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
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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")[] 
[1855]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1856]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1857]
Underfull \hbox (badness 1082) in paragraph at lines 2305--2309
[][][]\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;
[1858]
Underfull \hbox (badness 10000) in paragraph at lines 2342--2344
[]\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
Underfull \hbox (badness 1057) in paragraph at lines 2374--2381
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1859] [1860] [1861]
Underfull \hbox (badness 10000) in paragraph at lines 2563--2565
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1862] [1863] [1864] [1865]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2854--2857
[]\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
[1866]
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 []\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 '[] 
[1867]
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[]\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
[1868] [1869] [1870] [1871] [1872] [1873] [1874]
Underfull \hbox (badness 1072) in paragraph at lines 3484--3492
[]\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
[1875]
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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[]\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
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\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
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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1876] [1877]
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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 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down
load.file[][][] \T1/ptm/m/n/10 and
[1878] [1879] [1880]
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[]\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
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[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1881]
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 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
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\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1882] [1883] [1884] [1885] [1886]
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 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1887]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4373 ...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.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [1888] [1889] [1890]
[1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901]
[1902]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5326--5326
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1903]
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[]\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
[1904]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1905] [1906] [1907]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
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\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
[1908]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
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[]\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
[1909] [1910]
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[]\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
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1911]
Underfull \hbox (badness 5091) in paragraph at lines 5969--5971
[]\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
[1912]
Overfull \hbox (44.55087pt too wide) in paragraph at lines 5985--5990
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 
Overfull \hbox (48.30977pt too wide) in paragraph at lines 5998--6005
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
[1913]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
Underfull \hbox (badness 10000) in paragraph at lines 6115--6119
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
[1914]
Underfull \hbox (badness 2376) in paragraph at lines 6129--6136
[]\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 6129--6136
\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 6129--6136
\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 1314) in paragraph at lines 6188--6195
[]\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
[1915]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6252--6252
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1916]
Underfull \hbox (badness 5133) in paragraph at lines 6288--6292
[]\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 6302--6305
[]\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
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6349--6349
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1917] [1918]
Underfull \hbox (badness 4132) in paragraph at lines 6468--6470
[]\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
[1919] [1920] [1921]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6626--6626
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1922] [1923]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6769--6769
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1924]
Underfull \hbox (badness 10000) in paragraph at lines 6809--6811
[]\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
[1925] [1926]
Underfull \hbox (badness 10000) in paragraph at lines 6950--6952
[]\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 6955--6957
[]\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 class
[1927] [1928] [1929]
Underfull \hbox (badness 1859) in paragraph at lines 7178--7181
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1930]
Underfull \hbox (badness 1655) in paragraph at lines 7260--7263
[]\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
[1931]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7271--7271
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7275--7275
 []\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):[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 7283--7283
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1932]
Underfull \hbox (badness 10000) in paragraph at lines 7368--7372
[]\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1
0 is also al-lowed. If
[1933] [1934] [1935] [1936]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7632--7632
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7633--7633
 []            \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 7634--7634
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
[1937]
Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\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 7676--7678
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7684--7689
[]\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,
[1938]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7730--7730
 []          \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 7731--7731
 []                                   \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[] 
[1939] [1940]
Underfull \hbox (badness 10000) in paragraph at lines 7860--7865
[]\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 7860--7865
[][]\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 10000) in paragraph at lines 7867--7870
[]\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 7867--7870
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1941]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7983--7983
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7984--7984
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1942] [1943] [1944]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8155--8155
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1945]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[1946]
Underfull \hbox (badness 10000) in paragraph at lines 8336--8340
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8336--8340
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1947] [1948]
Underfull \hbox (badness 10000) in paragraph at lines 8451--8455
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8451--8455
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1949]
Underfull \hbox (badness 10000) in paragraph at lines 8516--8520
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8516--8520
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1950] [1951] [1952] [1953]
Underfull \hbox (badness 5203) in paragraph at lines 8847--8850
[]\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
[1954] [1955] [1956]
Underfull \hbox (badness 1776) in paragraph at lines 9073--9080
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1957]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9097--9097
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1958] [1959]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9258--9258
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1960] [1961]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9439--9439
 []\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[] 
[1962] [1963]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9525--9525
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9528--9528
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9533--9533
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1964]
Underfull \hbox (badness 1077) in paragraph at lines 9605--9608
[]\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
[1965] [1966] [1967] [1968] [1969] [1970]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10045--10045
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1971]
Underfull \hbox (badness 10000) in paragraph at lines 10132--10134
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1972] [1973]
Underfull \hbox (badness 2181) in paragraph at lines 10255--10259
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 10255--10259
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 10267--10271
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1974]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10285--10285
 []\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 10289--10289
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[1975] [1976]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10421--10421
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1977]
Underfull \hbox (badness 1917) in paragraph at lines 10544--10547
[]\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 10544--10547
\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
[1978]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 10567--10567
 []\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 '[] 
[1979]
Underfull \hbox (badness 8075) in paragraph at lines 10630--10632
[]\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
[1980]
Underfull \hbox (badness 6725) in paragraph at lines 10680--10689
\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,
Underfull \hbox (badness 6428) in paragraph at lines 10680--10689
\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 10680--10689
\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 10680--10689
\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
[1981]
Underfull \hbox (badness 3646) in paragraph at lines 10806--10808
[][][]$\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 /
[1982]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10844--10844
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[1983] [1984] [1985]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1986]
Underfull \hbox (badness 2012) in paragraph at lines 11151--11157
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use
[1987]
Underfull \hbox (badness 2096) in paragraph at lines 11164--11166
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 11167--11169
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 11174--11177
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 11178--11181
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11232--11232
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
[1988]
Underfull \hbox (badness 1009) in paragraph at lines 11250--11261
[]\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
[1989]
Underfull \hbox (badness 2846) in paragraph at lines 11337--11347
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 11476--11479
[]\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-
Underfull \hbox (badness 10000) in paragraph at lines 11476--11479
\T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 11493--11496
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1992]
Underfull \hbox (badness 2158) in paragraph at lines 11572--11575
[]\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
[1993] [1994] [1995]
Underfull \hbox (badness 3333) in paragraph at lines 11752--11754
[]\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-
[1996] [1997]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11917--11917
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
[1998]
Underfull \hbox (badness 5970) in paragraph at lines 11950--11953
[]\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 11950--11953
[][]\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 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1999]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12005--12005
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
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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[] 
[2000] [2001] [2002]
Underfull \hbox (badness 10000) in paragraph at lines 12213--12215
[]\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
[2003] [2004]
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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
Underfull \hbox (badness 6252) in paragraph at lines 12370--12377
\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 2452) in paragraph at lines 12370--12377
\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$"\T1/ptm/m/n/10 ) and
[2005] [2006] [2007]
Underfull \hbox (badness 2020) in paragraph at lines 12532--12548
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 12532--12548
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2008]
Underfull \hbox (badness 5022) in paragraph at lines 12642--12646
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2009] [2010] [2011]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12814--12814
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2012] [2013] [2014] [2015] [2016]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13178--13178
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13184--13184
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
[2017]
Underfull \hbox (badness 4467) in paragraph at lines 13205--13207
[]\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 13218--13222
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 13232--13236
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 13238--13243
[]\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 13238--13243
\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 13238--13243
\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 13244--13246
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
[2018]
Underfull \hbox (badness 10000) in paragraph at lines 13295--13300
[]\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 13303--13306
[][][]\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 ,
[2019]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13357--13357
 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2020] [2021] [2022]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13548
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 13561--13561
 []\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:[]
 
[2023]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13628--13628
 []                      \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)))[] 
[2024]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13669--13669
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
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[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[2025]
Underfull \hbox (badness 1715) in paragraph at lines 13721--13724
[]\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 13766--13768
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 13778--13782
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[2026] [2027] [2028]) [2029] [2030] (./KernSmooth-pkg.tex
Chapter 15.
[2031]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2032] [2033] [2034] [2035] [2036]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2037] [2038] [2039] [2040]) (./MASS-pkg.tex
Chapter 16.
[2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051]
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))[] 
[2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062]
[2063]
Underfull \hbox (badness 7256) in paragraph at lines 1603--1605
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411
 []\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"),[] 
[2075] [2076] [2077] [2078]
Underfull \hbox (badness 6559) in paragraph at lines 2693--2696
[]\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
[2079] [2080] [2081]
Underfull \hbox (badness 10000) in paragraph at lines 2863--2868
\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 8189) in paragraph at lines 2863--2868
\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 ,
Underfull \hbox (badness 3557) in paragraph at lines 2899--2907
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2899--2907
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2082] [2083]
Underfull \hbox (badness 4686) in paragraph at lines 3031--3033
[]\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
Underfull \hbox (badness 1515) in paragraph at lines 3045--3049
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2084] [2085] [2086]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
Underfull \hbox (badness 5817) in paragraph at lines 3233--3235
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2087]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098]
[2099]
Underfull \hbox (badness 1845) in paragraph at lines 4162--4164
[]\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
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2107] [2108]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2109]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2110] [2111] [2112] [2113] [2114]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
Underfull \hbox (badness 5022) in paragraph at lines 5292--5295
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2115]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5927--5927
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2124]
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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") 
[2125] [2126]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6130 ...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.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2127]
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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
[2128] [2129] [2130] [2131]
Underfull \vbox (badness 10000) has occurred while \output is active [2132]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6546--6546
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2133]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6634--6634
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2134] [2135] [2136] [2137] [2138] [2139]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7073--7073
 []\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 7090--7090
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2140]
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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 ) =
[2141]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2142] [2143]
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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
[2144] [2145]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7477--7477
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2146]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7542--7542
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2147] [2148] [2149] [2150] [2151] [2152]
Underfull \hbox (badness 4686) in paragraph at lines 7980--7982
[]\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
Underfull \hbox (badness 1515) in paragraph at lines 7996--8000
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2153] [2154]
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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 8123--8127
[]\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
[2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165]
[2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174]
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2175]
Underfull \hbox (badness 1158) in paragraph at lines 9629--9632
[]\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),
[2176]
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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)[] 
[2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187]
[2188] [2189]) (./Matrix-pkg.tex [2190]
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
[2191]
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
[2192]
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
[2193]
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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
[2194] [2195]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
Underfull \hbox (badness 5147) in paragraph at lines 495--498
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2196]
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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
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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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 546--546
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2197] [2198]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
 []\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 662--662
 []\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 675--675
 []        \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)]),[] 
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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2199]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2200] [2201] [2202]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2203]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-
Underfull \hbox (badness 10000) in paragraph at lines 1045--1050
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2204]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- '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.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2205pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ] [2206]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2207]
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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 1388--1391
[]\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
[2208]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\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
[2209]
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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[] 
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2210]
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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
Underfull \hbox (badness 3861) in paragraph at lines 1531--1538
\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
Underfull \hbox (badness 1783) in paragraph at lines 1566--1570
[]\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
[2211]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... 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.1623 ... 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.1624 \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.1645 \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.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2212]
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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
Underfull \hbox (badness 1237) in paragraph at lines 1721--1724
[][][]\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
[2213]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2214]
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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
[2215] [2216] [2217]
Underfull \hbox (badness 10000) in paragraph at lines 2112--2114
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2218] [2219]
Underfull \hbox (badness 10000) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
Underfull \hbox (badness 3068) in paragraph at lines 2295--2299
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2220]
Underfull \hbox (badness 4713) in paragraph at lines 2330--2332
[]\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
[2221]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2222]
Underfull \hbox (badness 10000) in paragraph at lines 2549--2553
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
[2223]
Underfull \hbox (badness 2707) in paragraph at lines 2605--2609
[]\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 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n 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 ;
[2224]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
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[]\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
[2225]
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[]\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 2713--2718
[][]\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
[2226]
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[]\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 2973--2974
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
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[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
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[]\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
[2227]
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class
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[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class
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[][][]\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
[2228] [2229]
Underfull \hbox (badness 1859) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
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[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2230]
Underfull \hbox (badness 1168) in paragraph at lines 3363--3366
[]\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
[2231] [2232]
Underfull \hbox (badness 4967) in paragraph at lines 3528--3532
[]\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
[2233]
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[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
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[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2234] [2235]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\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 10000) in paragraph at lines 3735--3737
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial
Underfull \hbox (badness 10000) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2236]
Underfull \hbox (badness 4967) in paragraph at lines 3813--3815
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3852--3855
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 1735) in paragraph at lines 3852--3855
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
[2237]
Underfull \hbox (badness 10000) in paragraph at lines 3855--3858
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 2318) in paragraph at lines 3855--3858
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
Underfull \hbox (badness 6364) in paragraph at lines 3859--3862
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2238]
Underfull \hbox (badness 4060) in paragraph at lines 3983--3986
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2239]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
[2240]
Underfull \hbox (badness 3635) in paragraph at lines 4091--4095
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2241] [2242] [2243] [2244]
Underfull \hbox (badness 10000) in paragraph at lines 4393--4398
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2245] [2246]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4544--4544
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2247] [2248]
Underfull \hbox (badness 10000) in paragraph at lines 4699--4701
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of 
a ma-trix, or the co-er-cions
[2249] [2250]
Underfull \hbox (badness 10000) in paragraph at lines 4846--4851
[]\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 ,
[2251]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4927--4927
 []\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 4929--4929
 []  \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 4933--4933
 []  \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 4940--4940
 []  \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 '[] 
[2252] [2253]
Underfull \hbox (badness 4120) in paragraph at lines 5079--5082
[]\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
[2254]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5116--5116
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5121--5121
 []\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 5128--5128
 []\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 5131--5131
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2255]
Underfull \hbox (badness 1817) in paragraph at lines 5220--5229
[]\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
Underfull \hbox (badness 5637) in paragraph at lines 5262--5264
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2256]
Underfull \hbox (badness 3138) in paragraph at lines 5288--5290
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2257]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5355--5355
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
Underfull \hbox (badness 1603) in paragraph at lines 5376--5378
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2258] [2259] [2260]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5613--5613
 []\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[] 
[2261]
Underfull \hbox (badness 10000) in paragraph at lines 5694--5697
[][][]\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 5705--5705
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2262]
Underfull \hbox (badness 1622) in paragraph at lines 5742--5747
[]\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 5742--5747
\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
[2263]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5803--5803
 []\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 5804--5804
 []          \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 5811--5811
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2264] [2265]
Underfull \hbox (badness 1062) in paragraph at lines 5940--5943
[]\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 2809) in paragraph at lines 5969--5972
[]\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
[2266]
Underfull \hbox (badness 2635) in paragraph at lines 6081--6086
[]\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 6081--6086
\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
[2267]
Underfull \hbox (badness 10000) in paragraph at lines 6089--6092
[]\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 6199--6209
\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 6199--6209
[][]\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
[2268]
Underfull \hbox (badness 1184) in paragraph at lines 6281--6284
[]\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
[2269]
Underfull \hbox (badness 10000) in paragraph at lines 6379--6382
[]\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.,
[2270]
Underfull \hbox (badness 10000) in paragraph at lines 6454--6457
[]\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.,
[2271]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6470--6470
 []\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 6509--6515
[]\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 6509--6515
[][]\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 6530--6533
[]\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
[2272]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6600--6600
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2273] [2274]
Underfull \hbox (badness 6268) in paragraph at lines 6736--6739
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2275]
Underfull \hbox (badness 5036) in paragraph at lines 6760--6764
[]\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 6760--6764
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6853 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 1348) in paragraph at lines 6933--6936
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
Underfull \hbox (badness 10000) in paragraph at lines 6938--6941
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
Underfull \hbox (badness 10000) in paragraph at lines 6938--6941
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
Underfull \hbox (badness 10000) in paragraph at lines 6956--6959
Underfull \hbox (badness 7326) in paragraph at lines 6966--6968
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re
-lies on a cor-rect
[2277]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.7029 ...*\%}{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.7137 ...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.7237 ...tcrossprod}{matrix-products}{tcrossprod}
                                                   [2278]
Underfull \hbox (badness 1881) in paragraph at lines 7335--7341
\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
[2279pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7397 \end{Details}
                    pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7397 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7408--7411
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 7408--7411
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 5637) in paragraph at lines 7411--7416
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
Underfull \hbox (badness 10000) in paragraph at lines 7420--7422
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
Underfull \hbox (badness 10000) in paragraph at lines 7422--7424
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2280] [2281]
Underfull \hbox (badness 1062) in paragraph at lines 7607--7610
[]\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
[2282]
Underfull \hbox (badness 2809) in paragraph at lines 7641--7644
[]\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
[2283]
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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/
ptm/m/n/10 should be done, af-ter
[2284]
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[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
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\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2285]
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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.,
[2287] [2288]
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[]\T1/ptm/m/n/10 fast
[2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8138 \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.8138 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2290]
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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 ,
[2291]
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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
[2292]
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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.,
[2293]
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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.,
[2294]
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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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[2295]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2296] [2297]
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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 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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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
[2298] [2299]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8938 \aliasA{qr}{qr-methods}{qr}
                                  
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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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![] 
[2300]
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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[] 
[2301]
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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
[2302]
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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"[] 
[2303]
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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.9234 ... the Reciprocal Condition Number}{rcond}
                                                   [2304]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2305] [2306] [2307]
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
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\T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2308] [2309]
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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
[2310]
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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:[] 
[2311]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9811 \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[] 
[2312]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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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 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
[2313]
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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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[] 
[2314]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form 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
[2315]
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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
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2316]
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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),[] 
[2317] [2318]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2319]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2320]
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[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
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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[] 
[2321]
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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)[] 
[2322]
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[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
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[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
[2323]
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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.10806 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2324] [2325]
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[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
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 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2326]
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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 ,
[2327]
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
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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
[2328]
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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
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2329] [2330]
Underfull \hbox (badness 3525) in paragraph at lines 11349--11353
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11356--11362
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2331]
Underfull \hbox (badness 10000) in paragraph at lines 11451--11455
[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
 \T1/ptm/m/it/10 sym-met-ric
Underfull \hbox (badness 1043) in paragraph at lines 11451--11455
[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
Underfull \hbox (badness 10000) in paragraph at lines 11467--11472
[]\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 1259) in paragraph at lines 11467--11472
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. 
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11475--11480
\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
[2332]
Underfull \hbox (badness 2057) in paragraph at lines 11547--11549
[]\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.,
[2333] [2334]
Underfull \hbox (badness 6641) in paragraph at lines 11633--11636
[]\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 11673--11677
[]\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 11673--11677
\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
[2335]
Underfull \hbox (badness 7649) in paragraph at lines 11780--11782
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2336] [2337] [2338]
Underfull \hbox (badness 7362) in paragraph at lines 11981--11983
[]\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
[2339]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12019--12019
 []\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 12020--12020
 []\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)[] 
[2340] [2341]
Underfull \hbox (badness 6910) in paragraph at lines 12270--12272
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2342] [2343] [2344]) (./boot-pkg.tex
Chapter 18.
[2345] [2346] [2347] [2348] [2349] [2350] [2351]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2352]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\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
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\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-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2353]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2354]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2355]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\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 851--855
[][][]\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 ,
[2356]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2357]
[2358]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2359]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\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 1082--1091
\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 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2360] [2361] [2362] [2363] [2364]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\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-
[2365] [2366] [2367] [2368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2369] [2370] [2371] [2372]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2373]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2374] [2375] [2376] [2377]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\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
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\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.
[2378]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\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 2437--2438
[][][]\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 ,
[2379]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\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 2533--2537
\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
[2380] [2381] [2382] [2383] [2384]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\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 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2385] [2386] [2387]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\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 ,
[2388]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2389] [2390] [2391]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2392] [2393] [2394] [2395] [2396] [2397] [2398]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2399] [2400]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2401] [2402] [2403]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\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 4368--4372
\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
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\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 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2429]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\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
[2430]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\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
[2431] [2432] [2433] [2434]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2435] [2436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\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 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2437] [2438] [2439]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\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
[2440] [2441]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex
[2450]
Chapter 19.
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex
Chapter 20.
[2467]
Underfull \hbox (badness 3098) in paragraph at lines 133--142
[]\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-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
 is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method 
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2468]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2469]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \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 253--253
 []  \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 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2470] [2471]
Underfull \vbox (badness 10000) has occurred while \output is active [2472]
[2473]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \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 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2474]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2475]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2476]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2477] [2478]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\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 
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2479]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2481]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\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 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2482]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2483]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1150--1150
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2484]
Underfull \hbox (badness 4144) in paragraph at lines 1182--1186
[]\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
[2485]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258
 []          \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 1264--1264
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2486] [2487]
Underfull \hbox (badness 10000) in paragraph at lines 1403--1408
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 1451--1454
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 1468--1472
[][][]\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 1492--1492
 []\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 1502--1502
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2489]
Underfull \hbox (badness 5741) in paragraph at lines 1542--1545
[]\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
[2490]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2491]
Underfull \hbox (badness 5008) in paragraph at lines 1725--1733
\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
[2492] [2493]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816
 []\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 1835--1835
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2494] [2495] [2496] [2497]
Underfull \hbox (badness 10000) in paragraph at lines 2143--2145
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 10000) in paragraph at lines 2154--2157
Underfull \hbox (badness 3179) in paragraph at lines 2168--2174
[][][]\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.
[2498] [2499] [2500]
Underfull \hbox (badness 10000) in paragraph at lines 2326--2329
[][][]\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 ,
[2501]
Underfull \hbox (badness 1292) in paragraph at lines 2394--2397
[]\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
Underfull \hbox (badness 6675) in paragraph at lines 2403--2405
[]\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 2426--2429
[][][]\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 ,
[2502] [2503] [2504] [2505]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642
 []\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 ):[] 
[2506] [2507]
Underfull \hbox (badness 1067) in paragraph at lines 2829--2834
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2508]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2509] [2510]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2511] [2512] [2513]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2514]
Underfull \hbox (badness 10000) in paragraph at lines 3255--3258
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2515]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2516] [2517] [2518]
Underfull \hbox (badness 10000) in paragraph at lines 3491--3494
[]\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
Underfull \hbox (badness 3471) in paragraph at lines 3491--3494
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2519]
Underfull \hbox (badness 10000) in paragraph at lines 3554--3559
[][][]\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 ,
[2520]
Underfull \hbox (badness 4621) in paragraph at lines 3616--3621
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3616--3621
\T1/ptm/m/n/10 which 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
Underfull \hbox (badness 6268) in paragraph at lines 3628--3631
[][][]\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 ,
[2521] [2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3816
[][][]\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 3844--3847
[][][]\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 ,
[2524]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3908--3910
[]\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
[2525] [2526] [2527] [2528]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101
 []     \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 4103--4103
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
Underfull \hbox (badness 1946) in paragraph at lines 4132--4137
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2529]
Underfull \hbox (badness 10000) in paragraph at lines 4199--4207
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2530]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241
 []\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 4250--4250
 []   \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 4252--4252
 []      \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 4255--4255
 []\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 4257--4257
 []   \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 4264--4264
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2531] [2532] [2533] [2534] [2535] [2536]
Underfull \hbox (badness 10000) in paragraph at lines 4622--4628
[]\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 4638--4640
[]\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 4651--4651
 []\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 4653--4653
 []\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)$id.med[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2537]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667
 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2538]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2539]
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[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2540]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2541] [2542] [2543]) (./foreign-pkg.tex [2544]
Chapter 22.
[2545]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2546] [2547]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\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 ,
[2548]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2549] [2550] [2551]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2552]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\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 506--515
\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
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1
0 ,
Underfull \hbox (badness 10000) in paragraph at lines 516--519
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-
Underfull \hbox (badness 10000) in paragraph at lines 516--519
\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
[2553]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\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
[2554]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
 []\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 625--625
 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2555]
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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 662--662
 []\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 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2556] [2557]
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2558] [2559]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2560]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
Underfull \hbox (badness 6708) in paragraph at lines 989--992
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2561] [2562]
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[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2563]
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[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2564]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\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 ,
[2565]
Underfull \hbox (badness 6725) in paragraph at lines 1293--1296
[]\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
[2566]) (./lattice-pkg.tex
Chapter 23.
[2567] [2568] [2569]
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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"),[] 
[2570]
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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"),[] 
[2571]
Underfull \hbox (badness 4060) in paragraph at lines 357--369
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both
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[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2572]
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[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2573] [2574]
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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
[2575] [2576] [2577] [2578]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\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.
[2579]
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
[2580] [2581]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2582] [2583] [2584]
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 ,
[2585]
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 ,
[2586]
Underfull \vbox (badness 10000) has occurred while \output is active [2587]
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
[2588]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\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
[2589]
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
[2590] [2591] [2592]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2593]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\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
[2594] [2595] [2596]
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"),[] 
Underfull \hbox (badness 4441) in paragraph at lines 2362--2366
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2597] [2598] [2599]
Underfull \hbox (badness 4441) in paragraph at lines 2547--2554
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2600] [2601]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689
 []          \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"),[] 
[2602]
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[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2603]
Underfull \hbox (badness 2913) in paragraph at lines 2791--2796
[]\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
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2877--2881
\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 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2604]
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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
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\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
[2605] [2606]
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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),[] 
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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"),[] 
[2607]
Underfull \hbox (badness 10000) in paragraph at lines 3110--3118
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\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 3143--3150
\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
[2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2612]
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2613] [2614] [2615] [2616] [2617]
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 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2618]
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\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2619] [2620]
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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
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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 4105--4109
\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
[2621]
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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 4170--4174
\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
[2622] [2623]
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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
[2624] [2625] [2626] [2627] [2628] [2629]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2630] [2631]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\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 .
[2632] [2633]
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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
[2634] [2635] [2636] [2637] [2638] [2639]
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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],[] 
[2640]
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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
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[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
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\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
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\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2641]
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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
[2642]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2643]
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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",[] 
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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
[2644]
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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
[2645]
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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
[2646] [2647]
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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 ,
[2648] [2649]
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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-
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Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\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 6273--6278
\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
[2652] [2653]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2654]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\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
[2655]
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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 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2656]
Underfull \hbox (badness 1005) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
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\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2657] [2658] [2659] [2660] [2661]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\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
[2662]
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2663]
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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
[2664]
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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
[2665] [2666]
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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
[2667]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2668] [2669]
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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
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\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
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\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-
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\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
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\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the
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\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2670]
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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),[] 
[2671]
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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)[] 
[2672] [2673] [2674]
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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")[] 
[2675]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\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 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
\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
[2684] [2685]
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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, ...)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2686]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\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
[2687]
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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
[2688]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2689] [2690]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2691] [2692]
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2693]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168
[]\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 (104.63074pt too wide) in paragraph at lines 9164--9168
\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
[2694] [2695] [2696] [2697] [2698] [2699] [2700]
Underfull \hbox (badness 4205) in paragraph at lines 9622--9626
[]\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 4518) in paragraph at lines 9622--9626
\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 ,
Underfull \hbox (badness 6300) in paragraph at lines 9627--9630
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2704] [2705] [2706]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
[]\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime
rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Cerebrovascular 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 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\
T1/ptm/m/n/10 , and
[2707]
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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2708]) (./mgcv-pkg.tex
Chapter 24.
[2709] [2710]
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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,[] 
[2711]
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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.
[2712] [2713] [2714] [2715]
Underfull \hbox (badness 10000) in paragraph at lines 358--365
[][][]\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 358--365
[][]\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 358--365
[][]\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 ,
[2716] [2717] [2718] [2719]
Underfull \hbox (badness 2922) in paragraph at lines 594--595
[]\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
[2720]
Underfull \hbox (badness 1158) in paragraph at lines 665--667
[]\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
[2721]
Underfull \hbox (badness 1259) in paragraph at lines 728--729
[]\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).
[2722] [2723] [2724] [2725] [2726] [2727] [2728]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1076--1076
 []\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)[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1083--1083
 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1090--1090
 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 
Overfull \hbox (74.58035pt too wide) in paragraph at lines 1092--1092
 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1094--1094
 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2729]
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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)[] 
[2730]
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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
[2732] [2733] [2734] [2735] [2736] [2737] [2738]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1685--1685
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2739] [2740] [2741] [2742] [2743] [2744]
Underfull \hbox (badness 1052) in paragraph at lines 2060--2068
\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
[2745]
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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
Underfull \hbox (badness 1142) in paragraph at lines 2102--2106
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
Underfull \hbox (badness 1043) in paragraph at lines 2128--2133
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2746] [2747] [2748]
Underfull \hbox (badness 1043) in paragraph at lines 2291--2297
\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
[2749] [2750]
Underfull \hbox (badness 10000) in paragraph at lines 2423--2429
[][][]\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 2423--2429
[][]\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 2423--2429
[][]\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 ,
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 []            \T1/pcr/m/n/10 keepData=FALSE,scale.est="fletcher",edge.correct=
FALSE)[] 
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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)),[] 
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Underfull \hbox (badness 5189) in paragraph at lines 3436--3440
[]\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
[2768]
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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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[2771]
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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)+[] 
[2780] [2781]
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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/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
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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 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 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
[2803]
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2804] [2805] [2806]
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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[2808]
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 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
[2815]
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
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[2823]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
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[2847]
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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 8237--8240
\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 8237--8240
\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 .
[2848]
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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 8293--8296
\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,[] 
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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
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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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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
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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
[2866]
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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 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,
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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,
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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.
[2874]
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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")[] 
[2875]
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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 ,
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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) 
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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, 
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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-
[2887]
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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/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
[2890] [2891]
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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
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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 ,
[2892] [2893] [2894]
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[][][]\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
[2895]
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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
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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
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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)[] 
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 []  \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs 
over (-.5,1.5)")[] 
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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/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[2900]
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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
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\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
[2901] [2902] [2903]
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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
[2904]
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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[] 
[2905]
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\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2906] [2907]
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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
[2908] [2909] [2910] [2911]
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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")[] 
Underfull \hbox (badness 10000) in paragraph at lines 12018--12020
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2912] [2913]
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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 12177--12180
\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 12177--12180
\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"
[2915] [2916]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12259--12259
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
Underfull \hbox (badness 10000) in paragraph at lines 12304--12310
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 12304--12310
\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-
[2917] [2918] [2919]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 12518--12518
 []\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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[2922]
Underfull \hbox (badness 10000) in paragraph at lines 12621--12629
[][][]\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 12647--12648
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2923] [2924] [2925] [2926]
Underfull \hbox (badness 3396) in paragraph at lines 12908--12911
[][][]\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
[2927]
Underfull \hbox (badness 10000) in paragraph at lines 12953--12955
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2928] [2929] [2930] [2931]
Underfull \hbox (badness 10000) in paragraph at lines 13177--13180
[]\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 13177--13180
\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
[2932]
Underfull \hbox (badness 10000) in paragraph at lines 13210--13214
[][][]\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 13210--13214
[][]\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 13210--13214
[][]\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 ,
[2933] [2934] [2935] [2936]
Underfull \hbox (badness 2158) in paragraph at lines 13451--13451
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2937]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 13526--13526
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2938] [2939]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13660--13660
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2940] [2941] [2942]
Underfull \hbox (badness 4846) in paragraph at lines 13791--13794
[]\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
[2943] [2944] [2945] [2946] [2947]
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[2949] [2950] [2951] [2952] [2953] [2954] [2955]
Underfull \hbox (badness 10000) in paragraph at lines 14616--14624
[]\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an
 ar-ray us-ing code like
Underfull \hbox (badness 10000) in paragraph at lines 14616--14624
\T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K)
[2956] [2957] [2958] [2959] [2960]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 14888--14888
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2961] [2962] [2963] [2964] [2965]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15182--15182
 []\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 15183--15183
 []\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 15195--15195
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[2966] [2967] [2968]) (./nlme-pkg.tex
Chapter 25.
[2969]
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
[2970]
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
[2971] [2972] [2973] [2974] [2975]
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,[] 
[2976] [2977]
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 ---------------------------
---------------[] 
[2978] [2979] [2980] [2981] [2982] [2983] [2984] [2985]
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 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[2986]
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
[2987] [2988] [2989] [2990] [2991] [2992] [2993]
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 ,
[2994]
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
[2995] [2996] [2997] [2998] [2999]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\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 ,
[3000]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3001]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3002] [3003]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\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 ,
[3004]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\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 ,
[3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023]
[3024]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\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 ,
[3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035]
[3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046]
[3047] [3048]
Underfull \hbox (badness 10000) in paragraph at lines 5159--5163
[][][]\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 ,
[3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 10000) in paragraph at lines 5476--5480
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5476--5480
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[3054] [3055]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5594
[][][]\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 ,
[3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064]
Underfull \hbox (badness 2799) in paragraph at lines 6097--6103
\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
[3065]
Underfull \hbox (badness 7133) in paragraph at lines 6158--6162
[]\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 ,
[3066]
Underfull \hbox (badness 2057) in paragraph at lines 6242--6253
[][][]\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 ,
[3067]
Underfull \hbox (badness 10000) in paragraph at lines 6306--6308
[]\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 6338--6338
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3068] [3069] [3070] [3071]
Underfull \hbox (badness 7133) in paragraph at lines 6556--6560
[]\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 ,
[3072]
Underfull \hbox (badness 10000) in paragraph at lines 6655--6661
[][][]\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 6682--6682
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3073]
Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3074]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3075] [3076] [3077]
Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
[][][]\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 ,
[3078]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7040--7042
[]\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
[3079] [3080] [3081]
Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
[][][]\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 ,
[3082] [3083] [3084]
Underfull \hbox (badness 10000) in paragraph at lines 7407--7415
[]\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 7407--7415
\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 1817) in paragraph at lines 7407--7415
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7430--7433
[][][]\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 ,
[3085] [3086] [3087]
Underfull \hbox (badness 3354) in paragraph at lines 7645--7647
[]\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
[3088] [3089] [3090] [3091] [3092] [3093]
Underfull \hbox (badness 1642) in paragraph at lines 8037--8059
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3094] [3095]
Underfull \hbox (badness 10000) in paragraph at lines 8157--8174
[][][]\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 8157--8174
[][]\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 ,
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 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8209--8231
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3096] [3097] [3098] [3099] [3100]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3101]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
 []\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.8565 \aliasA{sigma}{lmeObject}{sigma}
                                        [3102] [3103] [3104]
Underfull \hbox (badness 10000) in paragraph at lines 8726--8738
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113]
Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
[][][]\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 9328--9328
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3114]
Underfull \hbox (badness 6300) in paragraph at lines 9410--9413
[]\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
[3115] [3116] [3117] [3118]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9679 ...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.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3119]
Underfull \hbox (badness 10000) in paragraph at lines 9699--9702
[]\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 9743--9746
[]\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 9743--9746
\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
[3120] [3121] [3122]
Underfull \hbox (badness 2435) in paragraph at lines 9917--9922
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 7291) in paragraph at lines 10207--10209
[]\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
[3128] [3129] [3130]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3131]
Underfull \hbox (badness 1596) in paragraph at lines 10452--10478
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3132] [3133] [3134]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3135] [3136]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10790--10795
[]\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[][][]
[3137]
Underfull \hbox (badness 10000) in paragraph at lines 10812--10816
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
[]\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 10867--10867
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3138] [3139] [3140] [3141]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3142] [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152]
[3153]
Underfull \hbox (badness 6268) in paragraph at lines 11902--11912
[][][]\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 ,
[3154] [3155] [3156] [3157]
Underfull \hbox (badness 10000) in paragraph at lines 12163--12169
[][][]\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 ,
[3158] [3159] [3160] [3161] [3162]
Underfull \hbox (badness 6876) in paragraph at lines 12485--12487
[]\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
[3163] [3164]
Underfull \hbox (badness 2452) in paragraph at lines 12641--12648
[][][]\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 ,
[3165]
Underfull \hbox (badness 10000) in paragraph at lines 12706--12712
[][][]\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 ,
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176]
[3177] [3178] [3179]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3180]
Underfull \hbox (badness 10000) in paragraph at lines 13685--13688
[]\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
Underfull \hbox (badness 6016) in paragraph at lines 13713--13716
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13713--13716
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13720--13723
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13728--13735
[]\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 13728--13735
\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
[3181]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
Underfull \hbox (badness 10000) in paragraph at lines 13792--13795
[]\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 13792--13795
\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
[3182]
Underfull \hbox (badness 4582) in paragraph at lines 13820--13823
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13820--13823
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13824--13827
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3183]
Underfull \hbox (badness 10000) in paragraph at lines 13900--13903
[]\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
Underfull \hbox (badness 1472) in paragraph at lines 13925--13932
\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 ,
[3184]
Underfull \hbox (badness 10000) in paragraph at lines 13994--13996
[][][]\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 ,
[3185] [3186] [3187] [3188]
Underfull \hbox (badness 1540) in paragraph at lines 14209--14214
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3189] [3190] [3191] [3192] [3193]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202]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.15153 ...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.15153 ...Extract Random Effects}{random.effects}
                                                   [3203] [3204] [3205]
[3206] [3207] [3208] [3209] [3210] [3211] [3212]
Underfull \hbox (badness 1009) in paragraph at lines 15810--15819
\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
[3213] [3214] [3215]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3216] [3217] [3218] [3219]
Underfull \hbox (badness 10000) in paragraph at lines 16235--16253
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16235--16253
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3220]
Underfull \hbox (badness 10000) in paragraph at lines 16292--16298
[][][]\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 ,
[3221]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3222] [3223] [3224] [3225] [3226] [3227] [3228]
Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3229] [3230] [3231] [3232] [3233]
Underfull \hbox (badness 1867) in paragraph at lines 17147--17156
\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 17147--17156
\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"
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3234]
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3235] [3236] [3237] [3238]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17465
[][][]\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 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 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3239] [3240] [3241] [3242] [3243] [3244] [3245] [3246]
Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
[][][]\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 17993--18003
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18031--18036
\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
[3247]
Underfull \hbox (badness 3579) in paragraph at lines 18095--18100
\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
[3248]
Underfull \hbox (badness 3579) in paragraph at lines 18158--18163
\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
[3249]
Underfull \hbox (badness 1577) in paragraph at lines 18219--18221
[]\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 18221--18226
\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
[3250]
Underfull \hbox (badness 3579) in paragraph at lines 18284--18289
\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
[3251]
Underfull \hbox (badness 10000) in paragraph at lines 18317--18326
[][][]\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 18317--18326
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18356--18361
\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
[3252] [3253] [3254]
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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
[3255] [3256]
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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
[3257] [3258] [3259] [3260] [3261] [3262] [3263] [3264]) (./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}
                                                   [3265]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3266] [3267] [3268]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3269]
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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)),[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3270]
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\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3271]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3272]) (./rpart-pkg.tex
Chapter 27.
[3273] [3274] [3275] [3276]
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 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3277]
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[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3278] [3279] [3280]
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
[3281] [3282]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3283]
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[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3284]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3285]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3286] [3287] [3288]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\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 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3289]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\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
[3290]
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 []\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 1286--1286
 []\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 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3291] [3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\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 ',
[3297] [3298]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3299] [3300] [3301]) (./spatial-pkg.tex [3302]
Chapter 28.
[3303] [3304] [3305] [3306] [3307] [3308]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3309] [3310] [3311] [3312] [3313] [3314] [3315] [3316] [3317] [3318] [3319]
[3320] [3321]) (./survival-pkg.tex [3322]
Chapter 29.
[3323] [3324]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3325] [3326]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 278--278
 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 
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 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.319 ... 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.319 ... Myelogenous Leukemia survival data}{aml}
                                                   [3327] [3328]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 416--416
 []\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 418--418
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3329]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3330] [3331]
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 654--654
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 655--655
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3333] [3334]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 798--798
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3335] [3336] [3337]
Underfull \hbox (badness 1097) in paragraph at lines 968--970
[]\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 988--988
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3338] [3339]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1103--1103
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3340]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1171 ...erapy for Stage B/C colon cancer}{colon}
                                                  
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[3342] [3343] [3344] [3345] [3346]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1623--1623
 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3347] [3348] [3349] [3350] [3351]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1988--1988
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3352] [3353] [3354]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2237--2237
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3355] [3356] [3357] [3358] [3359]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2554--2554
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
Underfull \hbox (badness 1389) in paragraph at lines 2567--2569
[]\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
[3360]
Underfull \hbox (badness 1048) in paragraph at lines 2621--2623
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3361]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2698--2698
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3362] [3363] [3364] [3365]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2945--2945
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3366] [3367] [3368] [3369]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3211--3211
 []                    \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 )))[] 
[3370] [3371] [3372] [3373]
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[3375] [3376]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3620--3620
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3377] [3378]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3809--3809
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3379] [3380]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3925--3925
 []\T1/pcr/m/n/9 mresid <- (lung$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[] 
[3381]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4015--4015
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3382] [3383] [3384]
Underfull \hbox (badness 1852) in paragraph at lines 4163--4165
[]\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
[3385] [3386]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4297--4297
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4298--4298
 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3387] [3388]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3389]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4564--4564
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3390]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4585--4585
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3391] [3392]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4732--4732
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3393]
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[3395] [3396]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5029--5034
[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \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/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 5029--5034
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3397] [3398] [3399] [3400]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5302--5302
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 5303--5303
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3401]
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 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3402] [3403] [3404] [3405] [3406]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5693--5693
 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5694--5694
 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3407] [3408] [3409] [3410]
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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 ),[] 
[3411] [3412] [3413] [3414]
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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
[3415]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3416]
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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
Underfull \hbox (badness 3000) in paragraph at lines 6429--6431
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3417]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 6459--6459
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3418]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6545--6545
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3419] [3420] [3421]
Underfull \hbox (badness 10000) in paragraph at lines 6770--6775
[][][]\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 (18.78088pt too wide) in paragraph at lines 6791--6791
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3422] [3423] [3424]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3425]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3426] [3427]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3432]
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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/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
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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 )[] 
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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)[] 
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[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22] [23]
Underfull \hbox (badness 5862) in paragraph at lines 1379--1385
[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[24] [25] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1637--1637
 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n
ames and con-vert-ing col-umn names
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\T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T
1/ptm/m/n/10 ) is op-tional. Note that all
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\T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm
/m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1
/pcr/m/n/10 optional
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\T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing
 of
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[][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 .
 See also the
[27]
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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
[28]
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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
[29] [30]
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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)[] 
[31]
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[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())
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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
[32] [33]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34] [35]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
Underfull \hbox (badness 1107) in paragraph at lines 2358--2360
[]\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
[38] [39]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2525--2525
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[40] [41] [42]
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[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-
Underfull \hbox (badness 10000) in paragraph at lines 2690--2695
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56]
Underfull \hbox (badness 10000) in paragraph at lines 3648--3650
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[57] [58] [59]
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 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[60] [61] [62] [63]
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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
[64] [65]
Underfull \hbox (badness 4595) in paragraph at lines 4265--4268
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[66] [67]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4420--4420
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
[68]
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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-
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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
[69]
Underfull \hbox (badness 10000) in paragraph at lines 4541--4546
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for
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[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-
Underfull \hbox (badness 2181) in paragraph at lines 4541--4546
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[70]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4620--4620
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[71] [72] [73] [74]
Underfull \hbox (badness 2521) in paragraph at lines 4873--4875
[]\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
[75] [76] [77] [78] [79] [80]
Underfull \hbox (badness 10000) in paragraph at lines 5270--5278
[]\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
[81] [82] [83] [84] [85] [86] [87] [88]
Underfull \hbox (badness 1796) in paragraph at lines 5830--5838
[]\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 : / /
[89] [90]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6024--6024
 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 
Overfull \hbox (90.78033pt too wide) in paragraph at lines 6026--6026
 []\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 6027--6027
 []\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}[] 
[91] [92] [93]
Underfull \hbox (badness 1635) in paragraph at lines 6193--6196
[]\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
Underfull \hbox (badness 3009) in paragraph at lines 6197--6200
[]\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
Underfull \hbox (badness 1102) in paragraph at lines 6214--6227
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
Underfull \hbox (badness 1308) in paragraph at lines 6228--6236
[]\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
[94] [95]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6381--6381
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[96]
Overfull \hbox (107.35893pt too wide) in paragraph at lines 6423--6425
[]\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 : 
[97] [98]
Underfull \hbox (badness 10000) in paragraph at lines 6565--6568
[]\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 6565--6568
\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
[99] [100]
Underfull \hbox (badness 1248) in paragraph at lines 6747--6753
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-
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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
Underfull \hbox (badness 10000) in paragraph at lines 6767--6769
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[101]
Underfull \hbox (badness 1067) in paragraph at lines 6809--6816
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[102] [103]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 7001--7001
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[105]
Underfull \hbox (badness 1231) in paragraph at lines 7126--7132
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[106] [107] [108] [109]
Underfull \hbox (badness 10000) in paragraph at lines 7337--7339
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[110] [111]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7482--7482
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
Underfull \hbox (badness 4595) in paragraph at lines 7524--7527
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[112] [113] [114]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7720--7720
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[115] [116]
Underfull \hbox (badness 8132) in paragraph at lines 7821--7825
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The
Underfull \hbox (badness 4543) in paragraph at lines 7821--7825
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
Underfull \hbox (badness 10000) in paragraph at lines 7840--7850
[]\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 1062) in paragraph at lines 7840--7850
[][]\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
[117]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 7872--7876
[]\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")
Underfull \hbox (badness 7451) in paragraph at lines 7911--7921
[][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-
Underfull \hbox (badness 3449) in paragraph at lines 7911--7921
\T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10
 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a
m-
[118] [119] [120] [121] [122] [123]
Underfull \hbox (badness 10000) in paragraph at lines 8340--8352
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8340--8352
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[124] [125] [126]
Underfull \hbox (badness 5802) in paragraph at lines 8567--8571
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
Underfull \hbox (badness 10000) in paragraph at lines 8602--8603
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[127] [128] [129]
Underfull \hbox (badness 10000) in paragraph at lines 8787--8791
[]\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
[130]
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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 8877--8877
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 
[131]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 8902--8902
 []        \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"),[] 
[132] [133]
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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 9040--9042
[]\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
[134]
Underfull \hbox (badness 1132) in paragraph at lines 9112--9119
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[135]
Underfull \hbox (badness 1603) in paragraph at lines 9248--9251
[]\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
[136] [137] [138] [139] [140] [141] [142] [143] [144]
Underfull \hbox (badness 1917) in paragraph at lines 9854--9859
[]\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
[145]
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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 9910--9910
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[146] [147]
Underfull \hbox (badness 1168) in paragraph at lines 10012--10017
\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 10051--10057
[]\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
Underfull \hbox (badness 5403) in paragraph at lines 10058--10061
[]\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio
ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as
[148] [149] [150]
Underfull \hbox (badness 2828) in paragraph at lines 10217--10221
[][][]$\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 10217--10221
\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 / Double _
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10250--10250
 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[151] [152] [153] [154]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10465--10465
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[155]
Underfull \hbox (badness 1629) in paragraph at lines 10539--10543
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[156]
Underfull \hbox (badness 2150) in paragraph at lines 10640--10643
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[157]
Underfull \hbox (badness 3690) in paragraph at lines 10654--10662
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
Underfull \hbox (badness 3735) in paragraph at lines 10683--10690
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[158] [159] [160]
Underfull \hbox (badness 10000) in paragraph at lines 10879--10882
[]\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
[161] [162] [163] [164] [165] [166] [167] [168] [169]
Underfull \hbox (badness 5288) in paragraph at lines 11576--11578
[]\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 11586--11591
[]\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
[170]
Underfull \hbox (badness 10000) in paragraph at lines 11646--11648
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[171] [172]
Underfull \hbox (badness 4569) in paragraph at lines 11763--11767
[]\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
Underfull \hbox (badness 2401) in paragraph at lines 11763--11767
\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
[173] [174]
Underfull \hbox (badness 10000) in paragraph at lines 11878--11880
[]\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
Underfull \hbox (badness 2790) in paragraph at lines 11921--11923
[]\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10
 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1
0 is true, oth-er-wise
[175] [176] [177]
Underfull \hbox (badness 4048) in paragraph at lines 12092--12102
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is
Underfull \hbox (badness 3657) in paragraph at lines 12092--12102
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[178] [179] [180]
Underfull \hbox (badness 5460) in paragraph at lines 12340--12349
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-
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\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those
Underfull \hbox (badness 2707) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2818) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,
Underfull \hbox (badness 6978) in paragraph at lines 12340--12349
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[181] [182] [183] [184] [185]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12714--12714
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[186] [187] [188] [189]
Underfull \hbox (badness 5119) in paragraph at lines 12999--13002
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[190] [191]
Underfull \hbox (badness 2221) in paragraph at lines 13160--13169
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13421--13423
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[196] [197]
Underfull \hbox (badness 10000) in paragraph at lines 13536--13538
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 13686--13688
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13795--13799
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13806--13809
[][][]$\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 .
Overfull \hbox (47.58038pt too wide) in paragraph at lines 13827--13827
 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[202]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 13850--13850
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[203]
Underfull \hbox (badness 10000) in paragraph at lines 13942--13945
[][][]\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 13952--13952
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[204]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14027--14027
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[205]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 
Underfull \hbox (badness 7238) in paragraph at lines 14080--14087
[]\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 ,
Underfull \hbox (badness 10000) in paragraph at lines 14080--14087
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to
Underfull \hbox (badness 2126) in paragraph at lines 14080--14087
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-
Underfull \hbox (badness 3965) in paragraph at lines 14088--14092
[]\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,
[206] [207] [208]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14251--14251
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14252--14252
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[209]
Underfull \hbox (badness 10000) in paragraph at lines 14331--14335
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a
Underfull \hbox (badness 1389) in paragraph at lines 14331--14335
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[210] [211]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 14479--14479
 []\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 14482--14482
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[212]
Underfull \hbox (badness 1168) in paragraph at lines 14566--14570
[]\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-
Underfull \hbox (badness 2012) in paragraph at lines 14566--14570
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[213]
Underfull \hbox (badness 6944) in paragraph at lines 14661--14664
[][][]\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 ,
[214]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14686--14686
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[215] [216]
Underfull \hbox (badness 10000) in paragraph at lines 14820--14822
[]\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
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14839--14839
 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14841--14841
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 14844--14844
 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)))[] 
Underfull \hbox (badness 2790) in paragraph at lines 14850--14853
[]\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
[217]
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[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,
Underfull \hbox (badness 1024) in paragraph at lines 14881--14885
[]\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
[218]
Underfull \hbox (badness 10000) in paragraph at lines 14950--14952
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 14956--14960
[]\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,
Underfull \hbox (badness 10000) in paragraph at lines 14956--14960
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives
Underfull \hbox (badness 10000) in paragraph at lines 14961--14969
[]\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
Underfull \hbox (badness 3601) in paragraph at lines 14995--14999
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use
Underfull \hbox (badness 3302) in paragraph at lines 14995--14999
\T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[219]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15062--15062
 []\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 ")[] 
[220]
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 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan
t see the effect[] 
[221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15902--15902
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[233]
Underfull \hbox (badness 2418) in paragraph at lines 16011--16015
\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 16018--16021
[]\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
Underfull \hbox (badness 2326) in paragraph at lines 16046--16053
[][][]\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 ,
[234] [235] [236] [237]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
Underfull \hbox (badness 1867) in paragraph at lines 16317--16324
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[238] [239] [240] [241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16585--16585
 []  \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 [242]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 16614--16614
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 
[243]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16665--16665
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
Underfull \hbox (badness 10000) in paragraph at lines 16671--16675
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for
Underfull \hbox (badness 1028) in paragraph at lines 16671--16675
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[244] [245] [246] [247]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17030--17030
 []\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))) 
[248] [249] [250] [251]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17284--17284
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[252] [253] [254]
Underfull \hbox (badness 2435) in paragraph at lines 17545--17547
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[255]
Underfull \hbox (badness 1867) in paragraph at lines 17587--17594
[]\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1
0 has been built against ICU, it will only be used if
Underfull \hbox (badness 1490) in paragraph at lines 17587--17594
\T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n
/10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se-
Underfull \hbox (badness 1490) in paragraph at lines 17587--17594
\T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l
o-cale names). Note that
Underfull \hbox (badness 2285) in paragraph at lines 17602--17604
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17610--17610
 []\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.[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17620--17620
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 
[256]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 17640--17640
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[257] [258]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17774--17774
 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 17780--17780
 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17783--17783
 []\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 17789--17789
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[259] [260]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 17916--17916
 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17924--17924
 []\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):[] 
[261] [262] [263]
Underfull \hbox (badness 10000) in paragraph at lines 18129--18131
[]\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
[264]
Underfull \hbox (badness 4217) in paragraph at lines 18213--18222
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2057) in paragraph at lines 18228--18244
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 4699) in paragraph at lines 18642--18645
[]\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 ,
[271] [272]
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 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[273] [274]
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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Underfull \hbox (badness 1430) in paragraph at lines 19313--19318
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 19313--19318
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[282]
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher
Underfull \hbox (badness 10000) in paragraph at lines 19374--19379
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would
Underfull \hbox (badness 5008) in paragraph at lines 19374--19379
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to
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\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[283]
Underfull \hbox (badness 10000) in paragraph at lines 19434--19441
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If
Underfull \hbox (badness 6364) in paragraph at lines 19434--19441
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-
Underfull \hbox (badness 5064) in paragraph at lines 19434--19441
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with
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\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with
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[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[284]
Underfull \hbox (badness 1975) in paragraph at lines 19522--19525
[]\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
[285] [286] [287] [288] [289] [290]
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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
[291]
Underfull \hbox (badness 10000) in paragraph at lines 19931--19938
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20005--20009
[]\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-tory
[293]
Underfull \hbox (badness 10000) in paragraph at lines 20135--20139
[]\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 20135--20139
[][]\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
[294] [295]
Underfull \hbox (badness 10000) in paragraph at lines 20233--20240
[][][]\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 ,
[296] [297]
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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 loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use
[298]
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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 20424--20429
\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 20424--20429
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed
Underfull \hbox (badness 10000) in paragraph at lines 20424--20429
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[299] [300]
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20595--20595
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[301]
Underfull \hbox (badness 3343) in paragraph at lines 20651--20655
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[302]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20737--20737
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20748--20748
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[303] [304]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 20859--20859
 []\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 20862--20862
 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[] 
[305]
Underfull \hbox (badness 6380) in paragraph at lines 20907--20912
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be
Underfull \hbox (badness 1960) in paragraph at lines 20965--20972
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or
Underfull \hbox (badness 1043) in paragraph at lines 20965--20972
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in
[306]
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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
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21015--21015
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[307]
Underfull \hbox (badness 1205) in paragraph at lines 21038--21043
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[308]
Underfull \hbox (badness 1400) in paragraph at lines 21183--21187
[][][]\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
[309]
Overfull \hbox (36.83002pt too wide) in paragraph at lines 21203--21210
[]\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo
gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ;
Underfull \hbox (badness 4886) in paragraph at lines 21203--21210
\T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m
/n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the
[310] [311]
Underfull \hbox (badness 2469) in paragraph at lines 21353--21359
[]\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. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,
Underfull \hbox (badness 1939) in paragraph at lines 21353--21359
\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 names.
Underfull \hbox (badness 10000) in paragraph at lines 21353--21359
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[312] [313] [314] [315]
Underfull \hbox (badness 10000) in paragraph at lines 21670--21672
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[316] [317] [318] [319] [320]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 21974--21974
 []\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 21975--21975
 []        \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 21978--21978
 []\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)[] 
[321] [322]
Underfull \hbox (badness 1655) in paragraph at lines 22102--22106
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[323] [324] [325] [326]
Underfull \hbox (badness 2277) in paragraph at lines 22351--22354
[]\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.
[327] [328] [329] [330] [331] [332] [333]
Underfull \hbox (badness 10000) in paragraph at lines 22836--22842
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed
Underfull \hbox (badness 6316) in paragraph at lines 22836--22842
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[334]
Underfull \hbox (badness 1484) in paragraph at lines 22868--22876
[]\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 2951) in paragraph at lines 22868--22876
\T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http
s : / / www . microsoft . com / whdc /
Underfull \hbox (badness 3460) in paragraph at lines 22868--22876
\T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/
n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft .
[335]
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 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[336]
Underfull \hbox (badness 10000) in paragraph at lines 22999--23003
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-
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\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[337] [338] [339] [340] [341] [342]
Underfull \hbox (badness 10000) in paragraph at lines 23450--23458
\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 ;
[343] [344]
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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
[345]
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[]\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
Underfull \hbox (badness 10000) in paragraph at lines 23651--23654
[]\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 23651--23654
\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
[346] [347]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[348] [349] [350]
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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
[351] [352] [353] [354] [355] [356] [357]
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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
[358]
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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
[359]
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[]\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
[360]
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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:[] 
[361] [362] [363]
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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
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[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,
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\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[364]
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[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from
[365] [366]
Underfull \hbox (badness 1694) in paragraph at lines 25080--25083
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[367] [368] [369]
Underfull \hbox (badness 1603) in paragraph at lines 25327--25329
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[370] [371]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 25450--25458
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[372]
Underfull \hbox (badness 5475) in paragraph at lines 25587--25597
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to
[373]
Underfull \hbox (badness 3271) in paragraph at lines 25629--25632
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
Underfull \hbox (badness 10000) in paragraph at lines 25644--25646
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[374] [375] [376]
Underfull \hbox (badness 3138) in paragraph at lines 25907--25913
[]\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 25907--25913
\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 25907--25913
\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
Underfull \hbox (badness 1194) in paragraph at lines 25920--25923
[]\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 25944--25946
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
Underfull \hbox (badness 10000) in paragraph at lines 25956--25960
[]\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If
Underfull \hbox (badness 6592) in paragraph at lines 25956--25960
\T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen
t header. The de-fault is
Underfull \hbox (badness 10000) in paragraph at lines 25961--25967
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
[377]
Underfull \hbox (badness 3826) in paragraph at lines 25976--25981
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly
Overfull \hbox (49.4607pt too wide) in paragraph at lines 25982--25993
[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both
")
Underfull \hbox (badness 1009) in paragraph at lines 25994--25997
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 26004--26016
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
Underfull \hbox (badness 1072) in paragraph at lines 26004--26016
[][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar
e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a
Underfull \hbox (badness 10000) in paragraph at lines 26018--26025
[]\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 10000) in paragraph at lines 26018--26025
\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
Underfull \hbox (badness 6380) in paragraph at lines 26018--26025
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like
Overfull \hbox (34.78088pt too wide) in paragraph at lines 26018--26025
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[378] [379] [380] [381] [382]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26349--26349
 []\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 26362--26366
[]\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 26362--26366
\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)]
[383] [384] [385] [386] [387]
Underfull \hbox (badness 4341) in paragraph at lines 26686--26688
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4518) in paragraph at lines 26722--26728
[][][]\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
[388]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26744--26744
 []\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 26756--26756
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[389] [390] [391] [392] [393] [394] [395]
Underfull \hbox (badness 10000) in paragraph at lines 27190--27194
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[396]
Underfull \hbox (badness 1796) in paragraph at lines 27256--27259
[]\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
[397] [398] [399]
Underfull \hbox (badness 10000) in paragraph at lines 27453--27456
[]\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
[400] [401] [402] [403] [404] [405] [406] [407] [408]
Underfull \hbox (badness 1226) in paragraph at lines 28085--28090
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[409]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28130--28130
 []           \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))[] 
[410] [411] [412] [413]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28396--28396
 []\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 28407--28407
 []\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 28413--28413
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 28414--28414
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 28417--28417
 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[414]
Underfull \hbox (badness 7415) in paragraph at lines 28492--28496
[]\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
[415]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 28513--28513
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[416] [417]
Underfull \hbox (badness 2418) in paragraph at lines 28672--28683
[]\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
[418]
Underfull \hbox (badness 1248) in paragraph at lines 28806--28813
\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 28806--28813
\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 /
[419] [420]
Underfull \hbox (badness 1533) in paragraph at lines 28917--28920
[]\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
[421]
Underfull \hbox (badness 1337) in paragraph at lines 29014--29017
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[422]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29062--29062
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
Underfull \hbox (badness 1038) in paragraph at lines 29080--29091
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 29092--29095
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[423] [424]
Underfull \hbox (badness 1117) in paragraph at lines 29187--29193
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[425] [426] [427] [428] [429] [430]
Underfull \hbox (badness 4048) in paragraph at lines 29565--29570
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to
Underfull \hbox (badness 4582) in paragraph at lines 29565--29570
\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 29565--29570
\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 ,
[431] [432] [433] [434] [435] [436] [437] [438]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30111--30111
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[439] [440] [441] [442]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 30397--30399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[443] [444] [445]
Underfull \hbox (badness 7558) in paragraph at lines 30613--30617
[]\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 30623--30625
[]\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 5417) in paragraph at lines 30628--30631
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 30632--30634
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /
Underfull \hbox (badness 10000) in paragraph at lines 30635--30637
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[446] [447] [448] [449] [450] [451]
Underfull \hbox (badness 10000) in paragraph at lines 31040--31044
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[452] [453] [454] [455] [456]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31371--31371
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 31374--31374
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[457] [458] [459]
Underfull \hbox (badness 3375) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/
ptm/m/n/10 , are in-valid, e.g., du-
Underfull \hbox (badness 2359) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is 
back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal
Underfull \hbox (badness 2582) in paragraph at lines 31602--31609
\T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m
atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call
[460] [461] [462]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 31755--31755
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[463] [464]
Underfull \hbox (badness 10000) in paragraph at lines 31886--31890
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent
Underfull \hbox (badness 10000) in paragraph at lines 31886--31890
\T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE
), file =
[465] [466] [467]
Underfull \hbox (badness 2302) in paragraph at lines 32137--32144
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,
Underfull \hbox (badness 2837) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing
Underfull \hbox (badness 3815) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,
Underfull \hbox (badness 2181) in paragraph at lines 32137--32144
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[468]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32189--32189
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[469]
Underfull \hbox (badness 1158) in paragraph at lines 32293--32298
[]\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
[470]
Underfull \hbox (badness 10000) in paragraph at lines 32320--32326
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
Underfull \hbox (badness 1953) in paragraph at lines 32320--32326
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[471]
Underfull \hbox (badness 10000) in paragraph at lines 32396--32401
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
Underfull \hbox (badness 6725) in paragraph at lines 32396--32401
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[472]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32478--32478
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[473] [474] [475]
Underfull \hbox (badness 2809) in paragraph at lines 32742--32748
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment
Underfull \hbox (badness 7759) in paragraph at lines 32749--32752
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487]
Underfull \hbox (badness 1735) in paragraph at lines 33554--33560
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent
[488]
Underfull \hbox (badness 4303) in paragraph at lines 33570--33573
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[489] [490] [491] [492]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 33888--33888
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[493] [494] [495] [496]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34140--34140
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 
Overfull \hbox (42.78088pt too wide) in paragraph at lines 34142--34142
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[497]
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
[][][]\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
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
\T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T
1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-
Underfull \hbox (badness 10000) in paragraph at lines 34185--34191
\T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i
s the de-fault cur-rently;
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[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[498]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34296--34296
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[499] [500] [501]
Underfull \vbox (badness 10000) has occurred while \output is active [502]
[503]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34624--34624
 []\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 34639--34639
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[504] [505] [506] [507] [508] [509]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35078--35078
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35079--35079
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[510] [511] [512] [513]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 35343--35343
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[514]
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
[]\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 '
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want
Underfull \hbox (badness 8113) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call
Underfull \hbox (badness 10000) in paragraph at lines 35427--35437
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,
Underfull \hbox (badness 6542) in paragraph at lines 35427--35437
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on
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\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-
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\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or
[515]
Underfull \hbox (badness 10000) in paragraph at lines 35471--35477
[]\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 35471--35477
\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 35471--35477
\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 1728) in paragraph at lines 35483--35490
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 35483--35490
\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 35483--35490
\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
[516] [517] [518] [519] [520]
Underfull \hbox (badness 10000) in paragraph at lines 35824--35830
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[521] [522] [523]
Underfull \hbox (badness 1163) in paragraph at lines 36012--36019
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6
Underfull \hbox (badness 8132) in paragraph at lines 36012--36019
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[524] [525] [526] [527]
Underfull \hbox (badness 1142) in paragraph at lines 36275--36281
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 36290--36290
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[528] [529] [530]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36538--36538
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[531]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 36582--36582
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[532] [533] [534] [535] [536] [537] [538]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37016--37016
 []\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 37019--37019
 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[539]
Underfull \hbox (badness 10000) in paragraph at lines 37070--37077
[]\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 37070--37077
\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 ).
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37121--37121
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[540] [541] [542] [543]
Underfull \hbox (badness 2762) in paragraph at lines 37360--37369
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less
Underfull \hbox (badness 1466) in paragraph at lines 37360--37369
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple
[544]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 37422--37422
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[545] [546]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 37587--37587
 []\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. 
[547]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 37625--37625
 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 
[548]
Underfull \hbox (badness 3219) in paragraph at lines 37674--37679
[]\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 37674--37679
\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
[549]
Underfull \hbox (badness 2452) in paragraph at lines 37764--37767
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes
Underfull \hbox (badness 10000) in paragraph at lines 37764--37767
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 37951--37955
[]\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
Underfull \hbox (badness 1584) in paragraph at lines 37966--37969
[]\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
[553] [554]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 38098--38098
 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[555]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38168--38168
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[556] [557] [558]
Underfull \hbox (badness 1082) in paragraph at lines 38306--38309
[]\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
[559] [560]
Underfull \hbox (badness 1038) in paragraph at lines 38493--38496
[]\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
[561] [562] [563] [564] [565] [566]
Underfull \hbox (badness 1515) in paragraph at lines 38857--38860
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[567] [568] [569]
Underfull \hbox (badness 4096) in paragraph at lines 39098--39101
[]\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 ,
[570] [571]
Underfull \hbox (badness 10000) in paragraph at lines 39212--39216
[]\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.,
[572] [573]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 39365--39365
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 
Overfull \hbox (36.7804pt too wide) in paragraph at lines 39367--39367
 []            \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr
/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 39369--39369
 []                 \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n
/9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL
), dim=4, dimnames=list(as.character(2:5)))))[] 
[574]
Underfull \hbox (badness 10000) in paragraph at lines 39382--39384
[]\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
[575]
Underfull \hbox (badness 10000) in paragraph at lines 39462--39465
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[576] [577]
Underfull \hbox (badness 1867) in paragraph at lines 39580--39584
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / /
Underfull \hbox (badness 5475) in paragraph at lines 39642--39646
[][][]\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 \ [][]$\T1/pcr/m/n/10 https : / /
[578] [579] [580] [581] [582] [583] [584]
Underfull \hbox (badness 10000) in paragraph at lines 40060--40067
\T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/
n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', `
\T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ',
Underfull \hbox (badness 4467) in paragraph at lines 40116--40125
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 40116--40125
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
Underfull \hbox (badness 10000) in paragraph at lines 40126--40134
[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-
Underfull \hbox (badness 10000) in paragraph at lines 40126--40134
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at
Underfull \hbox (badness 1303) in paragraph at lines 40126--40134
\T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by
 de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[585]
Underfull \hbox (badness 1337) in paragraph at lines 40192--40200
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 40201--40204
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[586]
Underfull \hbox (badness 4429) in paragraph at lines 40258--40260
[][][]$\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[] 
[587] [588] [589]
Underfull \hbox (badness 10000) in paragraph at lines 40484--40486
[]\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
[590] [591]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40606--40606
 []\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 40608--40608
 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 
Underfull \vbox (badness 10000) has occurred while \output is active [592]
[593] [594] [595] [596]
Underfull \hbox (badness 6542) in paragraph at lines 40970--40972
[]\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
[597] [598] [599]
Underfull \hbox (badness 3460) in paragraph at lines 41136--41139
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via
Underfull \hbox (badness 1708) in paragraph at lines 41143--41151
[]\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 41143--41151
\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
Underfull \hbox (badness 10000) in paragraph at lines 41152--41156
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-
Underfull \hbox (badness 10000) in paragraph at lines 41152--41156
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like
Underfull \hbox (badness 3281) in paragraph at lines 41152--41156
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-
Underfull \hbox (badness 4859) in paragraph at lines 41173--41178
[][][]\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;
[600]
Underfull \hbox (badness 3895) in paragraph at lines 41235--41247
[]\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 41235--41247
\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 ,
[601] [602] [603]
Underfull \hbox (badness 10000) in paragraph at lines 41420--41423
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[604] [605]
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 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[606] [607] [608] [609] [610] [611]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42024--42024
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[612]
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 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[613]
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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
[614]
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[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be
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\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[615] [616]
Underfull \hbox (badness 3668) in paragraph at lines 42369--42371
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[617] [618]
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 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[619]
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 []\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[] 
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 []\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 ...[] 
[620] [621]
Underfull \hbox (badness 6220) in paragraph at lines 42686--42691
[]\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 42686--42691
\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 1533) in paragraph at lines 42686--42691
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,
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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
[622]
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[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[623]
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[]\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s
ame as
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\T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na.
rm = TRUE)) \T1/ptm/m/n/10 or
Underfull \hbox (badness 2818) in paragraph at lines 42792--42798
[]\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
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[624] [625]
Underfull \hbox (badness 1622) in paragraph at lines 42921--42923
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[626] [627] [628] [629]
Underfull \hbox (badness 10000) in paragraph at lines 43189--43194
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]
Underfull \hbox (badness 10000) in paragraph at lines 43189--43194
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
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\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[630]
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[]\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
[631]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 
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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
[632]) (./compiler-pkg.tex
Chapter 2.
[633]
Underfull \hbox (badness 2884) in paragraph at lines 101--115
[]\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
[634] [635] [636]) (./datasets-pkg.tex
Chapter 3.
Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[637] [638] [639] [640] [641]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[642]
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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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[644] [645] [646] [647]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[648] [649]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[650] [651]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\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.
[652] [653]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[654] [655] [656] [657] [658]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[659] [660]
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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 ,
Underfull \hbox (badness 2903) in paragraph at lines 1541--1544
\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
[661] [662] [663]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[664]
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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)[] 
[665] [666]
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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]]))))[] 
[667] [668] [669] [670]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[671] [672] [673] [674] [675] [676] [677] [678]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[679]
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[680]
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[682]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[683] [684]
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[685]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[686] [687] [688] [689] [690] [691] [692]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[693] [694]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[695]
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[696]
Underfull \hbox (badness 1173) in paragraph at lines 3876--3880
\T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [
][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 /
 datasets .
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[697]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 
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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
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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 /
[698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709]
[710] [711]) (./grDevices-pkg.tex [712]
Chapter 4.
[713] [714] [715] [716] [717] [718]
Underfull \hbox (badness 10000) in paragraph at lines 374--382
[]\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/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[719]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[720] [721] [722] [723] [724] [725] [726] [727] [728]
Underfull \hbox (badness 5175) in paragraph at lines 1082--1084
[]\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
[729]
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\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[730]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /
[731]
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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[732]
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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
[733] [734] [735]
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[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on
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\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of
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\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[736]
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[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when
Underfull \hbox (badness 10000) in paragraph at lines 1608--1612
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[737] [738] [739]
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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 1767--1772
\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
[740]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 
[741]
Underfull \hbox (badness 1184) in paragraph at lines 1891--1901
[]\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 ,
[742]
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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
[743] [744]
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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
[745] [746]
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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
[747] [748]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
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[756] [757] [758] [759] [760]
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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))[] 
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[761]
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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
[762] [763] [764]
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 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[765]
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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
[766]
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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
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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 ,
[771] [772] [773] [774] [775]
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\T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd
f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 
1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-
[776]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[778]
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[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[779] [780]
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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
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[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[781]
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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
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[782]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[783]
Underfull \hbox (badness 1755) in paragraph at lines 4739--4741
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[784] [785]
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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
[786] [787]
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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
[788]
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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
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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 ftp : / / ftp . gnu . org / pub / non-[]gnu /
[789] [790]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[791]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[792] [793]
Underfull \hbox (badness 10000) in paragraph at lines 5401--5403
[]\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
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[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[794] [795] [796] [797] [798]
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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
[799] [800] [801] [802] [803] [804] [805]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[806]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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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
[807]
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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
[808]
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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[809]
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[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[810]
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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 /
[811] [812] [813]
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\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via
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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
[814] [815] [816]) (./graphics-pkg.tex
Chapter 5.
Underfull \hbox (badness 10000) 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
[817] [818] [819] [820]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[821] [822] [823]
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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
[824] [825] [826]
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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
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[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[827]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[828] [829]
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[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[830] [831] [832] [833] [834] [835] [836]
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 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 
[837]
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\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 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground
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\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, 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 ),
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[838]
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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)[] 
[839] [840] [841] [842] [843]
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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
[844]
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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 = "")[] 
[845]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[846] [847]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[848] [849] [850] [851] [852]
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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
[853] [854] [855] [856] [857]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[858] [859]
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\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[860]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838
 []\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 :[] 
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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
[861]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[862] [863] [864]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091
 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 
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 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[865]
Underfull \hbox (badness 1755) in paragraph at lines 3161--3165
[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[866]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the
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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther
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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[867] [868] [869]
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
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par("fg"),[] 
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 FALSE,[] 
[870] [871] [872]
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ex = 0.8, adj = 0)[] 
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x = cexv[i])[] 
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 = c(0, 0.3))[] 
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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 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
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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
[875] [876]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[877]
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[878] [879]
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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
[880] [881] [882] [883]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[884]
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\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
[885]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 
[886]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[887]
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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 ,
[888] [889]
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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.
[890] [891]
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<"/builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/"mai.pdf, id=2932
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[893 </builddir/build/BUILD/R-3.5.0/library/graphics/help/figures/oma.pdf>]
[894]
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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
[895]
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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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[897]
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[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
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\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[898] [899] [900] [901]
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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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3"), border = FALSE)[] 
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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.,
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\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[902] [903] [904] [905] [906] [907] [908]
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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[] 
[909] [910] [911] [912] [913] [914]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[915] [916]
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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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[][] 
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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,[] 
[918]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 
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[920]
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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)))))[] 
[921]
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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
[922] [923] [924]
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[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[925]
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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))[] 
[926] [927] [928] [929] [930] [931]
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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):[] 
[932]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[933] [934] [935] [936] [937]
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us  =  FALSE,[] 
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us  =  FALSE,[] 
[938]
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, key.loc =  0:1,[] 
[939] [940]
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 NULL, ...)[] 
[941] [942]
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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
[943] [944]
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lambda = 2),[] 
[945] [946]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[947] [948]
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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�...")[] 
[949]
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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
[950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8789 \HeaderA{units}{Graphical Units}{units}
                                               [951]
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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
[952] [953]
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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)[] 
[954]) (./grid-pkg.tex
Chapter 6.
[955] [956] [957] [958] [959] [960]
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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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), name="B"),[] 
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), name="C"),[] 
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), name="D")),[] 
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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-
[972] [973] [974]
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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
[975] [976] [977] [978] [979] [980] [981]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[982] [983] [984]
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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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te"), name="r3")[] 
[985]
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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 ,
[986]
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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
[987] [988] [989]
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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
[990] [991] [992]
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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-
[993] [994] [995]
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="vp1::vp2")),[] 
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 NULL)[] 
[996] [997] [998] [999]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1000] [1001] [1002] [1003] [1004]
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t(name="vp2"))))[] 
[1005]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[1006]
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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
[1007] [1008]
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 NULL,[] 
[1009] [1010] [1011]
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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")[] 
[1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022]
[1023] [1024]
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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
[1025]
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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-
[1026] [1027] [1028]
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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
[1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037]
Underfull \hbox (badness 10000) in paragraph at lines 5189--5191
[]\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
[1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047]
Underfull \hbox (badness 3449) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1048] [1049] [1050] [1051] [1052]
Underfull \hbox (badness 1867) in paragraph at lines 6187--6189
[]\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
[1053]
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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 ,
[1054] [1055]
Underfull \hbox (badness 7649) in paragraph at lines 6356--6359
[]\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
[1056] [1057] [1058]
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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"))))[] 
[1059]) (./methods-pkg.tex [1060]
Chapter 7.
[1061] [1062]
Underfull \hbox (badness 1688) in paragraph at lines 166--171
\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
[1063] [1064] [1065]
Underfull \hbox (badness 1348) in paragraph at lines 392--395
[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1066] [1067]
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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[] 
[1068]
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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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[1071]
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[]\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o
r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 .
 Note
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\T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] 
\T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co
r-re-spond-ing col-
Underfull \hbox (badness 1789) in paragraph at lines 791--797
\T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr
/m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in
[1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082]
[1083] [1084]
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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/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1085] [1086]
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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
[1087] [1088] [1089]
Underfull \hbox (badness 1132) in paragraph at lines 2214--2219
[]\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 =
[1090] [1091]
Underfull \hbox (badness 10000) in paragraph at lines 2328--2332
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1092] [1093] [1094]
Underfull \hbox (badness 3792) in paragraph at lines 2574--2577
[]\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
Underfull \hbox (badness 1194) in paragraph at lines 2605--2609
[]\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
[1095]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1096] [1097] [1098]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1099] [1100] [1101] [1102] [1103] [1104] [1105]
Underfull \hbox (badness 10000) in paragraph at lines 3403--3408
[]\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,
Underfull \hbox (badness 6268) in paragraph at lines 3403--3408
\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
[1106] [1107]
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\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
[1108]
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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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[]
[1109] [1110]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))
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Underfull \hbox (badness 10000) in paragraph at lines 3809--3810
[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
[1111]
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[]\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = 
"Pos") 
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
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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
[1112] [1113] [1114]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1115] [1116]
Underfull \hbox (badness 1629) in paragraph at lines 4247--4256
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1117]
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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,[] 
[1118]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1119] [1120]
Underfull \hbox (badness 1033) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture
[1121]
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 ,
[1122] [1123] [1124]
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
[1125] [1126] [1127] [1128]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1129]
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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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[1131]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1132]
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[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1133]
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
[1134] [1135] [1136]
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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
[1137]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1138]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
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\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 10000) in paragraph at lines 6210--6226
[]\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
[1143] [1144]
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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
[1145]
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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
[1146]
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[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1147]
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][]\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
[1148]
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[1150] [1151]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}
                               [1152]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
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\T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the 
S4 bit of the ob-ject. With
[1153] [1154]
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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")[] 
[1155]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
[1156]
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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 ,
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\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 ,
[1157] [1158]
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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
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[]\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
[1159] [1160]
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[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-
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\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the
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\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't
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\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,
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\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171]
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[]\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
[1172]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1173]
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 =,[] 
[1174] [1175] [1176] [1177]
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[] 
[1178] [1179] [1180]
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")[] 
[1181] [1182]
Underfull \vbox (badness 2277) has occurred while \output is active [1183]
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[] 
[1184] [1185] [1186] [1187]
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[] 
[1188]
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][] 
[1189]
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][] 
[1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198]
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
[1199] [1200] [1201] [1202]) (./parallel-pkg.tex
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
[1203]
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
[1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 318--326
[]\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1
0 re-turns the num-ber of phys-i-cal cores and
[1207] [1208]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\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
[1209] [1210] [1211] [1212]
Underfull \hbox (badness 1917) in paragraph at lines 742--751
[]\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 742--751
\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
[1213] [1214]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824
 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1215]
Underfull \hbox (badness 10000) in paragraph at lines 884--887
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1216]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005
 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 
[1217]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009
 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1218]
Underfull \hbox (badness 5388) in paragraph at lines 1119--1124
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 1143--1151
[]\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
[1219]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180
 []\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)[] 
[1220] [1221]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296
 []                 \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 1310--1310
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
Underfull \hbox (badness 1577) in paragraph at lines 1339--1342
[]\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
[1222]
Underfull \hbox (badness 3375) in paragraph at lines 1385--1387
[]\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
[1223] [1224]) (./splines-pkg.tex
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
[1225] [1226] [1227] [1228] [1229] [1230] [1231]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1232] [1233] [1234] [1235]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1236] [1237] [1238]) (./stats-pkg.tex
Chapter 10.
[1239]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\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 ,
[1240] [1241] [1242] [1243] [1244]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1245] [1246] [1247] [1248] [1249] [1250] [1251]
Underfull \hbox (badness 1024) in paragraph at lines 847--849
[]\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
[1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 1391--1393
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1260]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class
Underfull \hbox (badness 1490) in paragraph at lines 1508--1512
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1261] [1262] [1263] [1264]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via
Underfull \hbox (badness 2197) in paragraph at lines 1773--1777
\T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-
[1265] [1266]
Underfull \hbox (badness 4303) in paragraph at lines 1874--1876
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues,
 see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/
pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with
[1267] [1268] [1269]
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure
Underfull \hbox (badness 10000) in paragraph at lines 2096--2101
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r
Underfull \hbox (badness 1371) in paragraph at lines 2096--2101
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous
Underfull \hbox (badness 1221) in paragraph at lines 2102--2108
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2102--2108
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1270] [1271]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1272] [1273] [1274]
Underfull \hbox (badness 1221) in paragraph at lines 2457--2462
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-
Underfull \hbox (badness 4608) in paragraph at lines 2457--2462
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1275]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1276] [1277]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1278] [1279] [1280] [1281]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1282] [1283] [1284]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 
[1285]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176
 []\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 3177--3177
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1286]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1287] [1288] [1289] [1290] [1291]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1292] [1293] [1294] [1295]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1296] [1297] [1298] [1299] [1300]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135
 []\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 4136--4136
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1301] [1302] [1303]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1304] [1305] [1306]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1307]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\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 =
[1308] [1309]
Underfull \hbox (badness 2080) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
Underfull \hbox (badness 2050) in paragraph at lines 4757--4763
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex-
ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me
th-ods, and \T1/pcr/m/n/10 coef
Underfull \hbox (badness 4954) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes
 should typ-i-cally also keep the \T1/pcr/m/n/10 complete = *
Underfull \hbox (badness 4726) in paragraph at lines 4757--4763
\T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe
f(obj, complete = TF))\T1/ptm/m/n/10 ,
[1310] [1311] [1312] [1313]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019
 []\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 5021--5021
 []\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))[] 
[1314]
Underfull \hbox (badness 7397) in paragraph at lines 5108--5112
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever
Underfull \hbox (badness 7326) in paragraph at lines 5108--5112
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1315] [1316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242
 []\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 5260--5260
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
Underfull \hbox (badness 2680) in paragraph at lines 5287--5289
[]\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
[1317]
Underfull \hbox (badness 10000) in paragraph at lines 5292--5294
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1318] [1319]
Underfull \hbox (badness 1436) in paragraph at lines 5470--5475
[]\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 5470--5475
\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 5470--5475
\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 ,
[1320] [1321] [1322]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5669--5669
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1323]
Underfull \hbox (badness 1168) in paragraph at lines 5741--5746
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1324] [1325]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5836--5836
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1326] [1327] [1328]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 6021--6021
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1329] [1330]
Underfull \hbox (badness 10000) in paragraph at lines 6184--6189
[]\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
[1331] [1332] [1333]
Underfull \hbox (badness 5954) in paragraph at lines 6380--6382
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1334]
Underfull \hbox (badness 2503) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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 6469--6474
\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,
[1335]
Underfull \hbox (badness 7238) in paragraph at lines 6505--6508
[][][]\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
[1336]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6540--6540
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6555--6555
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6570--6570
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 
[1337] [1338] [1339] [1340]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6814--6814
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1341] [1342]
Underfull \vbox (badness 10000) has occurred while \output is active [1343]
[1344] [1345] [1346]
Underfull \hbox (badness 10000) in paragraph at lines 7212--7216
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1347]
Underfull \hbox (badness 6493) in paragraph at lines 7311--7314
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1348] [1349]
Underfull \hbox (badness 10000) in paragraph at lines 7448--7451
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
[1350] [1351] [1352] [1353] [1354] [1355]
Underfull \hbox (badness 10000) in paragraph at lines 7858--7863
[]\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 , ...,
[1356] [1357]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7996--7998
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1358] [1359] [1360]
Underfull \hbox (badness 1210) in paragraph at lines 8213--8215
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8664--8664
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8686--8686
 []\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 8689--8689
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1368] [1369]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8827--8827
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1370]
Underfull \hbox (badness 1859) in paragraph at lines 8866--8871
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1371] [1372] [1373]
Underfull \hbox (badness 2865) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-
Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1374] [1375]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9254--9254
 []           \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 9255--9255
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1376] [1377] [1378]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9434--9436
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1379] [1380] [1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 2443) in paragraph at lines 9887--9893
[][][]\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);
[1386] [1387] [1388]
Underfull \hbox (badness 3758) in paragraph at lines 10100--10103
[]\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
[1389] [1390] [1391] [1392]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10336--10336
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1393]
Underfull \hbox (badness 4132) in paragraph at lines 10401--10405
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1394]
Underfull \hbox (badness 10000) in paragraph at lines 10506--10509
[]\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
[1395] [1396] [1397]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\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 ^^@
[1398]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1399]
Underfull \hbox (badness 10000) in paragraph at lines 10833--10839
[][][]\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 10871--10876
\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 (=
[1400] [1401]
Underfull \hbox (badness 2635) in paragraph at lines 11004--11007
\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
[1402] [1403] [1404]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
Underfull \hbox (badness 1337) in paragraph at lines 11208--11217
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-
Underfull \hbox (badness 3049) in paragraph at lines 11208--11217
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1405]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11290--11290
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1406]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11323--11323
 []            \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 11336--11340
[]\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
[1407] [1408] [1409]
Underfull \hbox (badness 7379) in paragraph at lines 11516--11519
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1410] [1411]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11655--11655
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1412]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11723--11723
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11735--11735
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 
[1413]
Underfull \hbox (badness 1062) in paragraph at lines 11784--11789
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 11801--11803
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1414] [1415]
Underfull \hbox (badness 3623) in paragraph at lines 11955--11957
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1416] [1417]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12051--12051
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1418]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12144--12144
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 12192--12195
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1420] [1421] [1422]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to
Underfull \hbox (badness 10000) in paragraph at lines 12394--12396
[]\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
[1423]
Underfull \hbox (badness 4739) in paragraph at lines 12417--12419
[]\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
[1424]
Underfull \hbox (badness 2753) in paragraph at lines 12486--12488
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1425] [1426]
Underfull \hbox (badness 1292) in paragraph at lines 12611--12615
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1427]
Underfull \hbox (badness 10000) in paragraph at lines 12724--12726
[]\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
Underfull \hbox (badness 2894) in paragraph at lines 12730--12734
[]\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 12730--12734
\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
[1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13437--13437
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1439]
Underfull \hbox (badness 4518) in paragraph at lines 13480--13485
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1440] [1441]
Underfull \hbox (badness 10000) in paragraph at lines 13679--13683
[]\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
 ,
[1442] [1443] [1444]
Underfull \hbox (badness 6995) in paragraph at lines 13864--13866
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1445] [1446]
Underfull \hbox (badness 1163) in paragraph at lines 14012--14020
\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 ,
[1447] [1448]
Underfull \hbox (badness 4518) in paragraph at lines 14132--14137
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1449] [1450]
Underfull \hbox (badness 10000) in paragraph at lines 14270--14274
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface =
Underfull \hbox (badness 7133) in paragraph at lines 14270--14274
\T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul
d the
[1451]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14318--14318
 []\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 14319--14319
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1452]
Underfull \hbox (badness 10000) in paragraph at lines 14374--14377
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,
Underfull \hbox (badness 1715) in paragraph at lines 14374--14377
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1453] [1454] [1455] [1456]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14662--14662
 []\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 14663--14663
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1457]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14713--14715
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14756--14756
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 2726) in paragraph at lines 15163--15166
[]\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 ,
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
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 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1476] [1477]
Underfull \hbox (badness 1014) in paragraph at lines 16016--16021
\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
[1478]
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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 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
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\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
[1479]
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 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 16718--16718
 []\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[] 
[1489] [1490] [1491]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16946--16946
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Underfull \hbox (badness 2359) in paragraph at lines 17507--17509
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1501]
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 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1504]
Underfull \hbox (badness 10000) in paragraph at lines 17759--17763
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1505]
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 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 
[1506]
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 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
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 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514]
Underfull \hbox (badness 1248) in paragraph at lines 18424--18427
[]\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
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\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to
[1515]
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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
Underfull \hbox (badness 2042) in paragraph at lines 18503--18505
[]\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
[1516] [1517]
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 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 
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 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
Overfull \hbox (123.1803pt too wide) in paragraph at lines 18669--18669
 []\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 18672--18672
 []\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 18692--18692
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 
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 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1519]
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[]\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 18730--18741
\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
[1520]
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 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1521] [1522] [1523]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19018--19018
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1524]
Underfull \hbox (badness 1337) in paragraph at lines 19094--19097
[]\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
[1525] [1526] [1527] [1528] [1529] [1530]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19413--19413
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1531]
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 []       \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 (6.78088pt too wide) in paragraph at lines 19504--19504
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1532]
Underfull \hbox (badness 3049) in paragraph at lines 19583--19587
[]\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
[1533] [1534] [1535] [1536]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19831--19831
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
Underfull \hbox (badness 4779) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for
Underfull \hbox (badness 1194) in paragraph at lines 19841--19844
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1537]
Underfull \hbox (badness 1107) in paragraph at lines 19899--19901
[]\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
[1538]
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 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1539]
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 []\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)[] 
Underfull \hbox (badness 10000) in paragraph at lines 20011--20014
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives
Underfull \hbox (badness 10000) in paragraph at lines 20011--20014
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for
[1540]
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 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1541] [1542]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20180--20180
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1543]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20245
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1544]
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 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
Underfull \hbox (badness 10000) in paragraph at lines 20346--20348
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 polym(*, coefs=<non-NULL>)\T1/ptm/m/n/10 , and
[1545]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20383--20383
 [] \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 20388--20388
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556]
[1557] [1558]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21238--21238
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1559]
Underfull \hbox (badness 6859) in paragraph at lines 21305--21312
[][][]\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 21316--21322
[]\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 ,
[1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570]
[1571]
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 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1572] [1573] [1574] [1575] [1576]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22338--22338
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 
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 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1577] [1578] [1579] [1580] [1581]
Underfull \hbox (badness 1337) in paragraph at lines 22662--22668
[]\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
[1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23214--23214
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1590] [1591]
Underfull \hbox (badness 1028) in paragraph at lines 23355--23358
[]\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
[1592] [1593]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
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[]\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
[1594]
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[]\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
[1595] [1596]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23684--23684
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1597] [1598] [1599]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23904--23904
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1600] [1601] [1602]
Underfull \hbox (badness 10000) in paragraph at lines 24050--24053
[]\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
Underfull \hbox (badness 2134) in paragraph at lines 24102--24106
[][][]\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
[1603]
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 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1604] [1605] [1606] [1607] [1608] [1609] [1610]
Underfull \hbox (badness 6268) in paragraph at lines 24581--24586
[][]\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 ,
[1611]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 24609--24609
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1612] [1613]
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[]\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 24799--24803
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 24799--24803
\T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1614]
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 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1615] [1616] [1617]
Underfull \hbox (badness 2495) in paragraph at lines 25025--25034
[]\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 [][]$\T1/pcr/m/n/10 https : / / en .
[1618]
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 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1619]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25201--25201
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 
[1620]
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 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda 
= NULL, cv = FALSE, 
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 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1621]
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[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
Underfull \hbox (badness 2435) in paragraph at lines 25271--25276
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1622]
Underfull \hbox (badness 2980) in paragraph at lines 25416--25418
[]\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g
iven, un-less it has been given as
[1623]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25452--25452
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
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 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars)  &  smoothi
ng splines")[] 
[1624]
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 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
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[1626]
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 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1627]
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 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1628] [1629] [1630] [1631] [1632] [1633]
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 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
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[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1634] [1635]
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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)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [1636]
Underfull \hbox (badness 2922) in paragraph at lines 26327--26332
[]\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
[1637]
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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),[] 
Overfull \hbox (42.18039pt too wide) in paragraph at lines 26367--26367
 []                    \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]),[] 
[1638]
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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/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),[] 
[1639]
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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
[1640]
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 []  \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 26546--26546
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 26556--26556
 []  \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 26561--26561
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1641]
Underfull \hbox (badness 2922) in paragraph at lines 26597--26603
[]\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(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26635--26635
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1642] [1643]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26749--26749
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1644]
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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
[1645]
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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")))[] 
[1646]
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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 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
[1647]
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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 ## 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")))[] 
[1648]
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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
[1649]
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 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 
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 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1650]
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[]\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
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 []\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)[] 
[1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658]
Underfull \hbox (badness 10000) in paragraph at lines 27679--27682
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-
Underfull \hbox (badness 10000) in paragraph at lines 27679--27682
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1659] [1660] [1661] [1662] [1663] [1664] [1665]
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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
[1666] [1667] [1668]
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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
[1669] [1670]
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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
[1671]
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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
[1672]
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 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1673] [1674]
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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)
[1675] [1676]
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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
[1677] [1678]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1679] [1680]
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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,[] 
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 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1681]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1682]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1683]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1684]
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[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1685]
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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
[1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693]
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 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1694]
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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1695] [1696] [1697] [1698]
Underfull \hbox (badness 10000) in paragraph at lines 30239--30243
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at
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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 30251--30251
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1699] [1700]
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 []\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:[] 
[1701] [1702] [1703] [1704]
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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
[1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712]
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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
[1713]
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[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1714] [1715] [1716] [1717] [1718]
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 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1719]
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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
[1720]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 31675--31675
 []\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 "")[] 
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 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1721]) (./stats4-pkg.tex [1722]
Chapter 11.
[1723] [1724] [1725]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1726] [1727] [1728]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1729]
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[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1730] [1731]) (./tcltk-pkg.tex [1732]
Chapter 12.
[1733] [1734] [1735] [1736]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1737] [1738] [1739]
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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
[1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751]
Underfull \hbox (badness 1189) in paragraph at lines 1407--1410
[][][]\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
[1752]) (./tools-pkg.tex
Chapter 13.
[1753]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1754]
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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
[1755]
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 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1756]
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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 ,
[1757]
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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
[1758] [1759] [1760] [1761] [1762] [1763] [1764]
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[1765] [1766]
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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")[] 
[1767] [1768]
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1769]
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[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1770]
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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
[1771]
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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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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1774] [1775] [1776] [1777] [1778]
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 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 
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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 .
[1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1782] [1783] [1784]
[1785]
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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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 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1786]
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 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
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
[1787]
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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
[1788]
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 
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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 .
[1789]
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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/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2423--2423
 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1790] [1791] [1792] [1793]
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 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1794]
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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
[1795] [1796] [1797] [1798] [1799]
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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
[1800] [1801] [1802] [1803] [1804]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3447--3447
 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1805] [1806] [1807] [1808]
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[]\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
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 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 
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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
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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
[1813]
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 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
[1814]
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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
[1815] [1816] [1817]
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 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 
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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
[1818]
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[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList
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\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if
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\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1819] [1820]
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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 ',
[1821]
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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 ',
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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
[1822] [1823] [1824]) (./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 ',
[1825] [1826] [1827]
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[]\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si
m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault
[1828]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1829]
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 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1830] [1831] [1832]
Underfull \hbox (badness 1946) in paragraph at lines 527--531
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
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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(),[] 
[1833]
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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-
[1834]
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 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1835]
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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
[1836]
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\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts
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\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1837]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1838]
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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
[1839] [1840]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1841]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1842] [1843] [1844] [1845] [1846]
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[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1847] [1848]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 
[1849]
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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1850]
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 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1851]
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1852]
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[]\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r
ors, by num-ber. It is best used with
[1853] [1854]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
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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")[] 
[1855]
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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1856]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1857]
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[][][]\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;
[1858]
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[]\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
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\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1859] [1860] [1861]
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[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1862] [1863] [1864] [1865]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing
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[][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n
/10 , and hence re-sult in a
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[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 2854--2857
[]\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
[1866]
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 []\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 '[] 
[1867]
Underfull \hbox (badness 2452) in paragraph at lines 3002--3005
[]\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
[1868] [1869] [1870] [1871] [1872] [1873] [1874]
Underfull \hbox (badness 1072) in paragraph at lines 3484--3492
[]\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
[1875]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\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 3540--3545
[]\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 3540--3545
\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 3540--3545
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1876] [1877]
Underfull \hbox (badness 4660) in paragraph at lines 3662--3665
\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 3686--3688
[]\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
[1878] [1879] [1880]
Underfull \hbox (badness 1565) in paragraph at lines 3871--3875
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3892--3898
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1881]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3954--3954
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
Overfull \hbox (2.55087pt too wide) in paragraph at lines 3982--3989
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1882] [1883] [1884] [1885] [1886]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4302--4302
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1887]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4373 ...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.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [1888] [1889] [1890]
[1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901]
[1902]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5326--5326
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1903]
Underfull \hbox (badness 10000) in paragraph at lines 5410--5412
[]\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
[1904]
Underfull \hbox (badness 1502) in paragraph at lines 5459--5464
[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1905] [1906] [1907]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\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 5632--5641
\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
[1908]
Underfull \hbox (badness 2150) in paragraph at lines 5695--5698
[]\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 5711--5714
[]\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
[1909] [1910]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1911]
Underfull \hbox (badness 5091) in paragraph at lines 5969--5971
[]\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
[1912]
Overfull \hbox (44.55087pt too wide) in paragraph at lines 5985--5990
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 
Overfull \hbox (48.30977pt too wide) in paragraph at lines 5998--6005
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")
[1913]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
Underfull \hbox (badness 10000) in paragraph at lines 6115--6119
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,
[1914]
Underfull \hbox (badness 2376) in paragraph at lines 6129--6136
[]\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 6129--6136
\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 6129--6136
\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 1314) in paragraph at lines 6188--6195
[]\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
[1915]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6252--6252
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1916]
Underfull \hbox (badness 5133) in paragraph at lines 6288--6292
[]\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 6302--6305
[]\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
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6349--6349
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1917] [1918]
Underfull \hbox (badness 4132) in paragraph at lines 6468--6470
[]\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
[1919] [1920] [1921]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6626--6626
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1922] [1923]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6769--6769
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1924]
Underfull \hbox (badness 10000) in paragraph at lines 6809--6811
[]\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
[1925] [1926]
Underfull \hbox (badness 10000) in paragraph at lines 6950--6952
[]\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 6955--6957
[]\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 class
[1927] [1928] [1929]
Underfull \hbox (badness 1859) in paragraph at lines 7178--7181
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1930]
Underfull \hbox (badness 1655) in paragraph at lines 7260--7263
[]\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
[1931]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7271--7271
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7275--7275
 []\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):[] 
Overfull \hbox (47.58038pt too wide) in paragraph at lines 7283--7283
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1932]
Underfull \hbox (badness 10000) in paragraph at lines 7368--7372
[]\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1
0 is also al-lowed. If
[1933] [1934] [1935] [1936]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7632--7632
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7633--7633
 []            \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 7634--7634
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 
[1937]
Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\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 7676--7678
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like
Underfull \hbox (badness 1259) in paragraph at lines 7684--7689
[]\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,
[1938]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7730--7730
 []          \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 7731--7731
 []                                   \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[] 
[1939] [1940]
Underfull \hbox (badness 10000) in paragraph at lines 7860--7865
[]\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 7860--7865
[][]\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 10000) in paragraph at lines 7867--7870
[]\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 7867--7870
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1941]
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7984--7984
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1942] [1943] [1944]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8155--8155
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1945]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[1946]
Underfull \hbox (badness 10000) in paragraph at lines 8336--8340
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8336--8340
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1947] [1948]
Underfull \hbox (badness 10000) in paragraph at lines 8451--8455
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8451--8455
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1949]
Underfull \hbox (badness 10000) in paragraph at lines 8516--8520
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion
Underfull \hbox (badness 10000) in paragraph at lines 8516--8520
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1950] [1951] [1952] [1953]
Underfull \hbox (badness 5203) in paragraph at lines 8847--8850
[]\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
[1954] [1955] [1956]
Underfull \hbox (badness 1776) in paragraph at lines 9073--9080
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set
[1957]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9097--9097
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1958] [1959]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9258--9258
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1960] [1961]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9439--9439
 []\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[] 
[1962] [1963]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9525--9525
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9528--9528
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9533--9533
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1964]
Underfull \hbox (badness 1077) in paragraph at lines 9605--9608
[]\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
[1965] [1966] [1967] [1968] [1969] [1970]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10045--10045
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1971]
Underfull \hbox (badness 10000) in paragraph at lines 10132--10134
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1972] [1973]
Underfull \hbox (badness 2181) in paragraph at lines 10255--10259
[]\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n
/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-
Underfull \hbox (badness 2269) in paragraph at lines 10255--10259
\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see
Underfull \hbox (badness 10000) in paragraph at lines 10267--10271
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1974]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10285--10285
 []\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 10289--10289
 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[1975] [1976]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10421--10421
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1977]
Underfull \hbox (badness 1917) in paragraph at lines 10544--10547
[]\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 10544--10547
\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
[1978]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 10567--10567
 []\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 '[] 
[1979]
Underfull \hbox (badness 8075) in paragraph at lines 10630--10632
[]\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
[1980]
Underfull \hbox (badness 6725) in paragraph at lines 10680--10689
\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,
Underfull \hbox (badness 6428) in paragraph at lines 10680--10689
\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 10680--10689
\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 10680--10689
\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
[1981]
Underfull \hbox (badness 3646) in paragraph at lines 10806--10808
[][][]$\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 /
[1982]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10844--10844
 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[1983] [1984] [1985]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1986]
Underfull \hbox (badness 2012) in paragraph at lines 11151--11157
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use
[1987]
Underfull \hbox (badness 2096) in paragraph at lines 11164--11166
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 2698) in paragraph at lines 11167--11169
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1527) in paragraph at lines 11174--11177
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if
Underfull \hbox (badness 1067) in paragraph at lines 11178--11181
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
Overfull \hbox (6.78088pt too wide) in paragraph at lines 11232--11232
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 
[1988]
Underfull \hbox (badness 1009) in paragraph at lines 11250--11261
[]\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
[1989]
Underfull \hbox (badness 2846) in paragraph at lines 11337--11347
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 11476--11479
[]\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-
Underfull \hbox (badness 10000) in paragraph at lines 11476--11479
\T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form
Underfull \hbox (badness 10000) in paragraph at lines 11493--11496
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1992]
Underfull \hbox (badness 2158) in paragraph at lines 11572--11575
[]\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
[1993] [1994] [1995]
Underfull \hbox (badness 3333) in paragraph at lines 11752--11754
[]\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-
[1996] [1997]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 11917--11917
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 
[1998]
Underfull \hbox (badness 5970) in paragraph at lines 11950--11953
[]\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 11950--11953
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
Underfull \hbox (badness 1052) in paragraph at lines 11961--11970
\T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f
aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons
;
[1999]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 12005--12005
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12036--12036
 []\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 12043--12043
 []\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 12045--12045
 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
 # "1 is 1" here[] 
[2000] [2001] [2002]
Underfull \hbox (badness 10000) in paragraph at lines 12213--12215
[]\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
[2003] [2004]
Underfull \hbox (badness 4492) in paragraph at lines 12370--12377
[]\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
Underfull \hbox (badness 6252) in paragraph at lines 12370--12377
\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 2452) in paragraph at lines 12370--12377
\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$"\T1/ptm/m/n/10 ) and
[2005] [2006] [2007]
Underfull \hbox (badness 2020) in paragraph at lines 12532--12548
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),
Underfull \hbox (badness 1194) in paragraph at lines 12532--12548
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[2008]
Underfull \hbox (badness 5022) in paragraph at lines 12642--12646
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th
e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl
e
Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2009] [2010] [2011]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12814--12814
 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2012] [2013] [2014] [2015] [2016]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13178--13178
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 13184--13184
 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 
[2017]
Underfull \hbox (badness 4467) in paragraph at lines 13205--13207
[]\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 13218--13222
\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
Overfull \hbox (36.87935pt too wide) in paragraph at lines 13232--13236
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 13238--13243
[]\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 13238--13243
\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 13238--13243
\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 13244--13246
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and
[2018]
Underfull \hbox (badness 10000) in paragraph at lines 13295--13300
[]\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 13303--13306
[][][]\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 ,
[2019]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13357--13357
 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2020] [2021] [2022]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13548
[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;
Overfull \hbox (42.18039pt too wide) in paragraph at lines 13561--13561
 []\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:[]
 
[2023]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13628--13628
 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13650--13650
 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2024]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13669--13669
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
Underfull \hbox (badness 1454) in paragraph at lines 13696--13700
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[2025]
Underfull \hbox (badness 1715) in paragraph at lines 13721--13724
[]\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 13766--13768
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
Underfull \hbox (badness 3271) in paragraph at lines 13778--13782
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if
[2026] [2027] [2028]) [2029] [2030] (./KernSmooth-pkg.tex
Chapter 15.
[2031]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2032] [2033] [2034] [2035] [2036]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2037] [2038] [2039] [2040]) (./MASS-pkg.tex
Chapter 16.
[2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051]
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))[] 
[2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062]
[2063]
Underfull \hbox (badness 7256) in paragraph at lines 1603--1605
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2411--2411
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2415--2415
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2075] [2076] [2077] [2078]
Underfull \hbox (badness 6559) in paragraph at lines 2693--2696
[]\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
[2079] [2080] [2081]
Underfull \hbox (badness 10000) in paragraph at lines 2863--2868
\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 8189) in paragraph at lines 2863--2868
\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 ,
Underfull \hbox (badness 3557) in paragraph at lines 2899--2907
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if
Underfull \hbox (badness 3118) in paragraph at lines 2899--2907
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[2082] [2083]
Underfull \hbox (badness 4686) in paragraph at lines 3031--3033
[]\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
Underfull \hbox (badness 1515) in paragraph at lines 3045--3049
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2084] [2085] [2086]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3226--3226
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
Underfull \hbox (badness 5817) in paragraph at lines 3233--3235
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[2087]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3356--3356
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098]
[2099]
Underfull \hbox (badness 1845) in paragraph at lines 4162--4164
[]\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
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2107] [2108]
Underfull \hbox (badness 10000) in paragraph at lines 4810--4813
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2109]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2110] [2111] [2112] [2113] [2114]
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[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if
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[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2115]
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[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123]
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 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2124]
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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") 
[2125] [2126]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6130 ...sical N, P, K Factorial Experiment}{npk}
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                   \relax 
l.6130 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2127]
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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
[2128] [2129] [2130] [2131]
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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)))[] 
[2133]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2134] [2135] [2136] [2137] [2138] [2139]
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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"))[] 
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2140]
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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 ) =
[2141]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2142] [2143]
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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
[2144] [2145]
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2146]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2147] [2148] [2149] [2150] [2151] [2152]
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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
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[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2153] [2154]
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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
[2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165]
[2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174]
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2175]
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[]\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),
[2176]
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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)[] 
[2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187]
[2188] [2189]) (./Matrix-pkg.tex [2190]
Chapter 17.
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[]\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
[2191]
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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
[2192]
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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
[2193]
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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
[2194] [2195]
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 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 
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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2196]
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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
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
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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)],[] 
[2197] [2198]
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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)]),[] 
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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2199]
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[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2200] [2201] [2202]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2203]
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-
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\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to
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\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of
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[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2204]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
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                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2205pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
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already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ] [2206]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2207]
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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
[2208]
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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
[2209]
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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[] 
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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2210]
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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
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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
[2211]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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                   \relax 
l.1624 \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.1645 \aliasA{rowMeans}{colSums}{rowMeans}
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                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2212]
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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
[2213]
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[]\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se
t the
[2214]
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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
[2215] [2216] [2217]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2218] [2219]
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[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =
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\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2220]
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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
[2221]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2222]
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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("dgTMatrix",    ...)\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or
[2223]
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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 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\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 ;
[2224]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\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 2677--2682
[]\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 2677--2682
[][]\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
[2225]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\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 2713--2718
[][]\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
[2226]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\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 2973--2974
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :
Underfull \hbox (badness 1810) in paragraph at lines 2980--2982
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of
Underfull \hbox (badness 10000) in paragraph at lines 2983--2985
[]\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 3803) in paragraph at lines 2986--2990
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a
[2227]
Underfull \hbox (badness 1371) in paragraph at lines 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\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 3012--3016
[][][]\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
[2228] [2229]
Underfull \hbox (badness 1859) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains
Underfull \hbox (badness 10000) in paragraph at lines 3243--3245
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2230]
Underfull \hbox (badness 1168) in paragraph at lines 3363--3366
[]\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
[2231] [2232]
Underfull \hbox (badness 4967) in paragraph at lines 3528--3532
[]\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
[2233]
Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
Underfull \hbox (badness 6364) in paragraph at lines 3575--3578
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2234] [2235]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\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 10000) in paragraph at lines 3735--3737
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial
Underfull \hbox (badness 10000) in paragraph at lines 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2236]
Underfull \hbox (badness 4967) in paragraph at lines 3813--3815
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 3852--3855
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 1735) in paragraph at lines 3852--3855
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the
[2237]
Underfull \hbox (badness 10000) in paragraph at lines 3855--3858
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or
Underfull \hbox (badness 2318) in paragraph at lines 3855--3858
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
Underfull \hbox (badness 6364) in paragraph at lines 3859--3862
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2238]
Underfull \hbox (badness 4060) in paragraph at lines 3983--3986
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2239]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 
[2240]
Underfull \hbox (badness 3635) in paragraph at lines 4091--4095
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
Underfull \hbox (badness 10000) in paragraph at lines 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2241] [2242] [2243] [2244]
Underfull \hbox (badness 10000) in paragraph at lines 4393--4398
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2245] [2246]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 
Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
Overfull \hbox (58.38037pt too wide) in paragraph at lines 4544--4544
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2247] [2248]
Underfull \hbox (badness 10000) in paragraph at lines 4699--4701
[][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of 
a ma-trix, or the co-er-cions
[2249] [2250]
Underfull \hbox (badness 10000) in paragraph at lines 4846--4851
[]\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 ,
[2251]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4927--4927
 []\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 4929--4929
 []  \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 4933--4933
 []  \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 4940--4940
 []  \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 '[] 
[2252] [2253]
Underfull \hbox (badness 4120) in paragraph at lines 5079--5082
[]\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
[2254]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5116--5116
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5121--5121
 []\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 5128--5128
 []\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 5131--5131
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2255]
Underfull \hbox (badness 1817) in paragraph at lines 5220--5229
[]\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
Underfull \hbox (badness 5637) in paragraph at lines 5262--5264
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2256]
Underfull \hbox (badness 3138) in paragraph at lines 5288--5290
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2257]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5355--5355
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
Underfull \hbox (badness 1603) in paragraph at lines 5376--5378
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as
Underfull \hbox (badness 10000) in paragraph at lines 5384--5389
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2258] [2259] [2260]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5613--5613
 []\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[] 
[2261]
Underfull \hbox (badness 10000) in paragraph at lines 5694--5697
[][][]\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 5705--5705
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2262]
Underfull \hbox (badness 1622) in paragraph at lines 5742--5747
[]\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 5742--5747
\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
[2263]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5803--5803
 []\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 5804--5804
 []          \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 5811--5811
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2264] [2265]
Underfull \hbox (badness 1062) in paragraph at lines 5940--5943
[]\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 2809) in paragraph at lines 5969--5972
[]\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
[2266]
Underfull \hbox (badness 2635) in paragraph at lines 6081--6086
[]\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 6081--6086
\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
[2267]
Underfull \hbox (badness 10000) in paragraph at lines 6089--6092
[]\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 6199--6209
\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 6199--6209
[][]\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
[2268]
Underfull \hbox (badness 1184) in paragraph at lines 6281--6284
[]\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
[2269]
Underfull \hbox (badness 10000) in paragraph at lines 6379--6382
[]\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.,
[2270]
Underfull \hbox (badness 10000) in paragraph at lines 6454--6457
[]\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.,
[2271]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6470--6470
 []\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 6509--6515
[]\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 6509--6515
[][]\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
[2272]
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 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2273] [2274]
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[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2275]
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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 ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
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                   \relax 
l.6853 \aliasA{det}{Matrix-class}{det}
                                      
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[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when
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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.7029 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7137 ...A{crossprod}{matrix-products}{crossprod}
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                   \relax 
l.7237 ...tcrossprod}{matrix-products}{tcrossprod}
                                                   [2278]
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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
[2279pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7397 \end{Details}
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                                                  \fi \fi 
l.7397 \end{Details}
                    ]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-
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\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
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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
[2282]
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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
[2283]
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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/
ptm/m/n/10 should be done, af-ter
[2284]
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[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not
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\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2285]
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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.,
[2287] [2288]
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[]\T1/ptm/m/n/10 fast
[2289]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8138 \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.8138 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2290]
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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 ,
[2291]
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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
[2292]
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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.,
[2293]
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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.,
[2294]
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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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[2295]
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[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use
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[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse
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\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2296] [2297]
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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 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
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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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Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8938 \aliasA{qr}{qr-methods}{qr}
                                  
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[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with
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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![] 
[2300]
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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[] 
[2301]
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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
[2302]
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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"[] 
[2303]
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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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<to be read again> 
                   \relax 
l.9234 ... the Reciprocal Condition Number}{rcond}
                                                   [2304]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2305] [2306] [2307]
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
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\T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When
[2308] [2309]
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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
[2310]
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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:[] 
[2311]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9811 \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[] 
[2312]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods
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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 basically com-putes uses tri-an-gu-lar
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list
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\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-
[2313]
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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing
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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[] 
[2314]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form 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-
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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
[2315]
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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
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2316]
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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),[] 
[2317] [2318]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 
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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2319]
Underfull \hbox (badness 4621) in paragraph at lines 10467--10471
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2320]
Underfull \hbox (badness 10000) in paragraph at lines 10543--10546
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10555--10555
 []\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 10559--10559
 []\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 10560--10560
 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10565--10565
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10568--10568
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2321]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10591--10591
 []\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 10592--10592
 []\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 10618--10618
 []\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 10620--10620
 []   \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 10622--10622
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2322]
Underfull \hbox (badness 10000) in paragraph at lines 10715--10723
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
Underfull \hbox (badness 1325) in paragraph at lines 10736--10740
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a
[2323]
Underfull \hbox (badness 10000) in paragraph at lines 10766--10770
[][][]\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.10806 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2324] [2325]
Underfull \hbox (badness 1430) in paragraph at lines 10936--10938
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10964--10964
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
Underfull \hbox (badness 5036) in paragraph at lines 10992--10994
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2326]
Underfull \hbox (badness 2970) in paragraph at lines 11125--11131
[]\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 11125--11131
\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 ,
[2327]
Underfull \hbox (badness 10000) in paragraph at lines 11176--11179
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
Underfull \hbox (badness 10000) in paragraph at lines 11198--11201
[]\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
[2328]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11221
[]\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 11231--11233
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2329] [2330]
Underfull \hbox (badness 3525) in paragraph at lines 11349--11353
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
Underfull \hbox (badness 1831) in paragraph at lines 11356--11362
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u
sual con-struc-tor of such ma-tri-ces. Then,
[2331]
Underfull \hbox (badness 10000) in paragraph at lines 11451--11455
[]\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns
 \T1/ptm/m/it/10 sym-met-ric
Underfull \hbox (badness 1043) in paragraph at lines 11451--11455
[][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 
Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This
Underfull \hbox (badness 10000) in paragraph at lines 11467--11472
[]\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 1259) in paragraph at lines 11467--11472
\T1/pcr/m/n/10 list(NULL, <character>)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. 
How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other
Underfull \hbox (badness 2591) in paragraph at lines 11475--11480
\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
[2332]
Underfull \hbox (badness 2057) in paragraph at lines 11547--11549
[]\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.,
[2333] [2334]
Underfull \hbox (badness 6641) in paragraph at lines 11633--11636
[]\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 11673--11677
[]\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 11673--11677
\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
[2335]
Underfull \hbox (badness 7649) in paragraph at lines 11780--11782
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2336] [2337] [2338]
Underfull \hbox (badness 7362) in paragraph at lines 11981--11983
[]\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
[2339]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12019--12019
 []\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 12020--12020
 []\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)[] 
[2340] [2341]
Underfull \hbox (badness 6910) in paragraph at lines 12270--12272
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2342] [2343] [2344]) (./boot-pkg.tex
Chapter 18.
[2345] [2346] [2347] [2348] [2349] [2350] [2351]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2352]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\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
Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\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-
Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2353]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2354]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2355]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\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 851--855
[][][]\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 ,
[2356]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2357]
[2358]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2359]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\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 1082--1091
\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 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2360] [2361] [2362] [2363] [2364]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\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-
[2365] [2366] [2367] [2368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2369] [2370] [2371] [2372]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
Underfull \vbox (badness 10000) has occurred while \output is active [2373]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2374] [2375] [2376] [2377]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\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
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\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.
[2378]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\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 2437--2438
[][][]\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 ,
[2379]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\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 2533--2537
\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
[2380] [2381] [2382] [2383] [2384]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\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 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2385] [2386] [2387]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\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 ,
[2388]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2389] [2390] [2391]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2392] [2393] [2394] [2395] [2396] [2397] [2398]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2399] [2400]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2401] [2402] [2403]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2405] [2406]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\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 4368--4372
\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
Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2416] [2417] [2418] [2419]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\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 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2420]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2429]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\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
[2430]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\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
[2431] [2432] [2433] [2434]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2435] [2436]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
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 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2437] [2438] [2439]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\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
[2440] [2441]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex
[2450]
Chapter 19.
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex
Chapter 20.
[2467]
Underfull \hbox (badness 3098) in paragraph at lines 133--142
[]\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-
Underfull \hbox (badness 2253) in paragraph at lines 133--142
\T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10
 is spec-i-fied of longer length than one. Since
Underfull \hbox (badness 3323) in paragraph at lines 133--142
\T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val
id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror
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\T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n
/10 . Fur-ther, \T1/pcr/m/n/10 method= "single"
Underfull \hbox (badness 10000) in paragraph at lines 133--142
\T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method 
= c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and
Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2468]
Underfull \hbox (badness 10000) in paragraph at lines 167--169
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2469]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \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 253--253
 []  \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 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2470] [2471]
Underfull \vbox (badness 10000) has occurred while \output is active [2472]
[2473]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \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 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2474]
Underfull \hbox (badness 5374) in paragraph at lines 539--541
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2475]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2476]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2477] [2478]
Underfull \hbox (badness 2941) in paragraph at lines 778--781
[][][]\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 
,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2479]
Underfull \hbox (badness 10000) in paragraph at lines 863--865
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2481]
Underfull \hbox (badness 4872) in paragraph at lines 974--976
[]\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 988--992
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2482]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2483]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1150--1150
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2484]
Underfull \hbox (badness 4144) in paragraph at lines 1182--1186
[]\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
[2485]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258
 []          \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 1264--1264
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2486] [2487]
Underfull \hbox (badness 10000) in paragraph at lines 1403--1408
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 1451--1454
[2488]
Underfull \hbox (badness 10000) in paragraph at lines 1468--1472
[][][]\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 1492--1492
 []\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 1502--1502
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2489]
Underfull \hbox (badness 5741) in paragraph at lines 1542--1545
[]\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
[2490]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2491]
Underfull \hbox (badness 5008) in paragraph at lines 1725--1733
\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
[2492] [2493]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816
 []\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 1835--1835
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2494] [2495] [2496] [2497]
Underfull \hbox (badness 10000) in paragraph at lines 2143--2145
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as
Underfull \hbox (badness 10000) in paragraph at lines 2154--2157
Underfull \hbox (badness 3179) in paragraph at lines 2168--2174
[][][]\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.
[2498] [2499] [2500]
Underfull \hbox (badness 10000) in paragraph at lines 2326--2329
[][][]\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 ,
[2501]
Underfull \hbox (badness 1292) in paragraph at lines 2394--2397
[]\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
Underfull \hbox (badness 6675) in paragraph at lines 2403--2405
[]\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 2426--2429
[][][]\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 ,
[2502] [2503] [2504] [2505]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642
 []\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 ):[] 
[2506] [2507]
Underfull \hbox (badness 1067) in paragraph at lines 2829--2834
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2508]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2509] [2510]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2511] [2512] [2513]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2514]
Underfull \hbox (badness 10000) in paragraph at lines 3255--3258
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2515]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2516] [2517] [2518]
Underfull \hbox (badness 10000) in paragraph at lines 3491--3494
[]\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
Underfull \hbox (badness 3471) in paragraph at lines 3491--3494
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2519]
Underfull \hbox (badness 10000) in paragraph at lines 3554--3559
[][][]\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 ,
[2520]
Underfull \hbox (badness 4621) in paragraph at lines 3616--3621
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1990) in paragraph at lines 3616--3621
\T1/ptm/m/n/10 which 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
Underfull \hbox (badness 6268) in paragraph at lines 3628--3631
[][][]\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 ,
[2521] [2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3816
[][][]\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 3844--3847
[][][]\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 ,
[2524]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 
Underfull \hbox (badness 2035) in paragraph at lines 3908--3910
[]\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
[2525] [2526] [2527] [2528]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101
 []     \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 4103--4103
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
Underfull \hbox (badness 1946) in paragraph at lines 4132--4137
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col
[2529]
Underfull \hbox (badness 10000) in paragraph at lines 4199--4207
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by
[2530]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241
 []\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 4250--4250
 []   \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 4252--4252
 []      \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 4255--4255
 []\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 4257--4257
 []   \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 4264--4264
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2531] [2532] [2533] [2534] [2535] [2536]
Underfull \hbox (badness 10000) in paragraph at lines 4622--4628
[]\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 4638--4640
[]\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 4651--4651
 []\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 4653--4653
 []\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)$id.med[] 
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 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 
[2537]
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 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2538]) (./codetools-pkg.tex
Chapter 21.
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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 
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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 
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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2539]
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[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2540]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2541] [2542] [2543]) (./foreign-pkg.tex [2544]
Chapter 22.
[2545]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2546] [2547]
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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 ,
[2548]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2549] [2550] [2551]
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 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2552]
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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/1
0 ,
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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
[2553]
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
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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
[2554]
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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,[] 
[2555]
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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="")[] 
[2556] [2557]
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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2558] [2559]
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 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2560]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 
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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2561] [2562]
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[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .
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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2563]
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[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2564]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\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 ,
[2565]
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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
[2566]) (./lattice-pkg.tex
Chapter 23.
[2567] [2568] [2569]
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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"),[] 
[2570]
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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"),[] 
[2571]
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[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the
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\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |
Underfull \hbox (badness 1028) in paragraph at lines 397--412
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both
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[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2572]
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[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2573] [2574]
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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
[2575] [2576] [2577] [2578]
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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.
[2579]
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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
[2580] [2581]
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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
[2582] [2583] [2584]
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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 ,
[2585]
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 ,
[2586]
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 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 
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[]\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
[2588]
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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
[2589]
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[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2590] [2591] [2592]
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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
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[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form
Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2593]
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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
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\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2594] [2595] [2596]
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"),[] 
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[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2597] [2598] [2599]
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[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2600] [2601]
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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"),[] 
[2602]
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[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2603]
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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.
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\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
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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
[2604]
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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
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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
[2605] [2606]
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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),[] 
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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"),[] 
[2607]
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[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x
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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.
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\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
[2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2612]
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2613] [2614] [2615] [2616] [2617]
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 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2618]
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\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2619] [2620]
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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
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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
[2621]
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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,
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\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
[2622] [2623]
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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
Underfull \hbox (badness 5231) in paragraph at lines 4284--4294
\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
Underfull \hbox (badness 1701) in paragraph at lines 4309--4312
[]\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 4312--4314
[]\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
[2624] [2625] [2626] [2627] [2628] [2629]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2630] [2631]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\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 .
[2632] [2633]
Underfull \hbox (badness 1442) in paragraph at lines 5035--5038
[]\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
[2634] [2635] [2636] [2637] [2638] [2639]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\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
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397
 []              \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],[] 
[2640]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\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 5486--5489
\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
Underfull \hbox (badness 6412) in paragraph at lines 5503--5509
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as
Underfull \hbox (badness 10000) in paragraph at lines 5503--5509
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2641]
Underfull \hbox (badness 1635) in paragraph at lines 5512--5517
[]\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
[2642]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2643]
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684
 []               \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",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 
Underfull \hbox (badness 10000) in paragraph at lines 5710--5712
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
[2644]
Underfull \hbox (badness 2376) in paragraph at lines 5721--5723
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2645]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\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 5857--5864
[]\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 5857--5864
\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
[2646] [2647]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\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 ,
[2648] [2649]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2650] [2651]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\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 6273--6278
\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
[2652] [2653]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2654]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\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
[2655]
Underfull \hbox (badness 10000) in paragraph at lines 6549--6552
[]\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 6549--6552
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2656]
Underfull \hbox (badness 1005) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to
Underfull \hbox (badness 1571) in paragraph at lines 6599--6607
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2657] [2658] [2659] [2660] [2661]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\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 6955--6962
\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
[2662]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2663]
Underfull \hbox (badness 10000) in paragraph at lines 7055--7059
[]\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 7055--7059
\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
[2664]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\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
[2665] [2666]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2667]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2668] [2669]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\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 7526--7529
[]\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
Underfull \hbox (badness 4242) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly
Underfull \hbox (badness 1147) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-
Underfull \hbox (badness 2351) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-
Underfull \hbox (badness 1675) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the
Underfull \hbox (badness 1769) in paragraph at lines 7540--7548
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2670]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2671]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2672] [2673] [2674]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2675]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\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
Underfull \hbox (badness 1231) in paragraph at lines 7912--7918
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
\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
[2684] [2685]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2686]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\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
[2687]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2688]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2689] [2690]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2691] [2692]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2693]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168
[]\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 (104.63074pt too wide) in paragraph at lines 9164--9168
\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
[2694] [2695] [2696] [2697] [2698] [2699] [2700]
Underfull \hbox (badness 4205) in paragraph at lines 9622--9626
[]\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 4518) in paragraph at lines 9622--9626
\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 ,
Underfull \hbox (badness 6300) in paragraph at lines 9627--9630
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2704] [2705] [2706]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
[]\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime
rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Cerebrovascular 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 ,
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T
1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\
T1/ptm/m/n/10 , and
[2707]
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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2708]) (./mgcv-pkg.tex
Chapter 24.
[2709] [2710]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\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,[] 
[2711]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152
 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\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.
[2712] [2713] [2714] [2715]
Underfull \hbox (badness 10000) in paragraph at lines 358--365
[][][]\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 358--365
[][]\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 ,
[2716] [2717] [2718] [2719]
Underfull \hbox (badness 2922) in paragraph at lines 594--595
[]\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
[2720]
Underfull \hbox (badness 1158) in paragraph at lines 665--667
[]\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
[2721]
Underfull \hbox (badness 1259) in paragraph at lines 728--729
[]\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).
[2722] [2723] [2724] [2725] [2726] [2727] [2728]
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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)[] 
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 
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 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 
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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",ylim=c(0,1),[] 
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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)[] 
[2730]
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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 
[2732] [2733] [2734] [2735] [2736] [2737] [2738]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2739] [2740] [2741] [2742] [2743] [2744]
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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
[2745]
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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 2089--2092
[]\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
Underfull \hbox (badness 1142) in paragraph at lines 2102--2106
\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.
[2746] [2747] [2748]
Underfull \hbox (badness 1043) in paragraph at lines 2291--2297
\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
[2749] [2750]
Underfull \hbox (badness 10000) in paragraph at lines 2423--2429
[][][]\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 2423--2429
[][]\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 2423--2429
[][]\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 ,
[2751]
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[2754] [2755] [2756]
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 []            \T1/pcr/m/n/10 keepData=FALSE,scale.est="fletcher",edge.correct=
FALSE)[] 
[2757] [2758] [2759] [2760] [2761]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3075--3075
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2762] [2763] [2764] [2765] [2766] [2767]
Underfull \hbox (badness 5189) in paragraph at lines 3436--3440
[]\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
[2768]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 3553--3553
 []\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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[2771]
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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
[2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779]
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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)+[] 
[2780] [2781]
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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, 
[2782] [2783]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
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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
[2784]
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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
[2785] [2786]
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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 ( []
[]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
[2787]
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[2789] [2790]
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2791] [2792] [2793] [2794] [2795] [2796] [2797]
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 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2798] [2799] [2800] [2801] [2802]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 
[2803]
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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2804] [2805] [2806]
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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 []\T1/pcr/m/n/9 jm <-jags.model("test.jags",data=jd$jags.data,inits=jd$jags.in
i,n.chains=1)[] 
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[2808]
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 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE) 
[2809] [2810] [2811]
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[2813] [2814]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 
[2815]
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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2816] [2817] [2818] [2819] [2820] [2821]
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[2823]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2824] [2825] [2826] [2827]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 
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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 
[2828] [2829] [2830] [2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
[2839] [2840] [2841] [2842] [2843] [2844] [2845]
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[2847]
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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 8237--8240
\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 8237--8240
\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 .
[2848]
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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
[2849] [2850] [2851]
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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,[] 
[2852] [2853] [2854]
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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
[2855] [2856] [2857]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2858] [2859] [2860] [2861] [2862] [2863]
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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
[2866]
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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
[2867]
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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,
[2868] [2869] [2870]
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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,
[2871] [2872] [2873]
Underfull \hbox (badness 1946) in paragraph at lines 9817--9824
[]\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.
[2874]
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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")[] 
[2875]
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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 ,
[2876] [2877] [2878] [2879] [2880]
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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) 
[2881] [2882] [2883] [2884] [2885]
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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, 
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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-
[2887]
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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-
[2888] [2889]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10749--10749
 [] \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 10760--10765
[]\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
[2890] [2891]
Underfull \hbox (badness 1803) in paragraph at lines 10837--10841
\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 10849--10861
\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
Underfull \hbox (badness 2401) in paragraph at lines 10866--10870
\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 10866--10870
\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 ,
[2892] [2893] [2894]
Underfull \hbox (badness 6876) in paragraph at lines 11061--11067
[][][]\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
[2895]
Underfull \hbox (badness 10000) in paragraph at lines 11102--11103
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2896] [2897]
Underfull \hbox (badness 10000) in paragraph at lines 11220--11221
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2898] [2899]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11274--11274
 []  \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 11286--11286
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11297--11297
 []  \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs 
over (-.5,1.5)")[] 
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11298--11298
 []  \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 11303--11303
 []  \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 11309--11309
 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11310--11310
 []  \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/
pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] 
[2900]
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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
Underfull \hbox (badness 10000) in paragraph at lines 11379--11381
\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
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 11507--11508
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2904]
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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[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11589--11589
 []\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[] 
[2905]
Underfull \hbox (badness 7613) in paragraph at lines 11627--11630
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 11736--11737
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2908] [2909] [2910] [2911]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11973--11973
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
Underfull \hbox (badness 10000) in paragraph at lines 12018--12020
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2912] [2913]
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Underfull \hbox (badness 10000) in paragraph at lines 12177--12180
[]\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 12177--12180
\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 12177--12180
\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"
[2915] [2916]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12259--12259
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
Underfull \hbox (badness 10000) in paragraph at lines 12304--12310
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 2698) in paragraph at lines 12304--12310
\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-
[2917] [2918] [2919]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 12518--12518
 []\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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[2922]
Underfull \hbox (badness 10000) in paragraph at lines 12621--12629
[][][]\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 12647--12648
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2923] [2924] [2925] [2926]
Underfull \hbox (badness 3396) in paragraph at lines 12908--12911
[][][]\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
[2927]
Underfull \hbox (badness 10000) in paragraph at lines 12953--12955
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2928] [2929] [2930] [2931]
Underfull \hbox (badness 10000) in paragraph at lines 13177--13180
[]\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 13177--13180
\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
[2932]
Underfull \hbox (badness 10000) in paragraph at lines 13210--13214
[][][]\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 13210--13214
[][]\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 13210--13214
[][]\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 ,
[2933] [2934] [2935] [2936]
Underfull \hbox (badness 2158) in paragraph at lines 13451--13451
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2937]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 13526--13526
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2938] [2939]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13660--13660
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2940] [2941] [2942]
Underfull \hbox (badness 4846) in paragraph at lines 13791--13794
[]\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
[2943] [2944] [2945] [2946] [2947]
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[2949] [2950] [2951] [2952] [2953] [2954] [2955]
Underfull \hbox (badness 10000) in paragraph at lines 14616--14624
[]\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an
 ar-ray us-ing code like
Underfull \hbox (badness 10000) in paragraph at lines 14616--14624
\T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K)
[2956] [2957] [2958] [2959] [2960]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 14888--14888
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2961] [2962] [2963] [2964] [2965]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15182--15182
 []\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 15183--15183
 []\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 15195--15195
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[2966] [2967] [2968]) (./nlme-pkg.tex
Chapter 25.
[2969]
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
[2970]
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
[2971] [2972] [2973] [2974] [2975]
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,[] 
[2976] [2977]
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 ---------------------------
---------------[] 
[2978] [2979] [2980] [2981] [2982] [2983] [2984] [2985]
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"),[] 
[2986]
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
[2987] [2988] [2989] [2990] [2991] [2992] [2993]
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 ,
[2994]
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
[2995] [2996] [2997] [2998] [2999]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\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 ,
[3000]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3001]
Underfull \hbox (badness 1132) in paragraph at lines 2144--2146
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3002] [3003]
Underfull \hbox (badness 4168) in paragraph at lines 2255--2261
[][][]\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 ,
[3004]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3005] [3006] [3007] [3008] [3009] [3010] [3011] [3012]
Underfull \hbox (badness 10000) in paragraph at lines 2843--2847
[][][]\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 ,
[3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023]
[3024]
Underfull \hbox (badness 6493) in paragraph at lines 3579--3587
[][][]\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 ,
[3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035]
[3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046]
[3047] [3048]
Underfull \hbox (badness 10000) in paragraph at lines 5159--5163
[][][]\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 ,
[3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 10000) in paragraph at lines 5476--5480
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if
Underfull \hbox (badness 2671) in paragraph at lines 5476--5480
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[3054] [3055]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5594
[][][]\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 ,
[3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064]
Underfull \hbox (badness 2799) in paragraph at lines 6097--6103
\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
[3065]
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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 ,
[3066]
Underfull \hbox (badness 2057) in paragraph at lines 6242--6253
[][][]\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 ,
[3067]
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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
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3068] [3069] [3070] [3071]
Underfull \hbox (badness 7133) in paragraph at lines 6556--6560
[]\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 ,
[3072]
Underfull \hbox (badness 10000) in paragraph at lines 6655--6661
[][][]\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 6682--6682
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3073]
Underfull \hbox (badness 10000) in paragraph at lines 6720--6722
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3074]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3075] [3076] [3077]
Underfull \hbox (badness 10000) in paragraph at lines 6993--7000
[][][]\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 ,
[3078]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
Underfull \hbox (badness 2875) in paragraph at lines 7040--7042
[]\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
[3079] [3080] [3081]
Underfull \hbox (badness 10000) in paragraph at lines 7255--7260
[][][]\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 ,
[3082] [3083] [3084]
Underfull \hbox (badness 10000) in paragraph at lines 7407--7415
[]\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 7407--7415
\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 1817) in paragraph at lines 7407--7415
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 
20 EM it-er-a-
Underfull \hbox (badness 3118) in paragraph at lines 7430--7433
[][][]\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 ,
[3085] [3086] [3087]
Underfull \hbox (badness 3354) in paragraph at lines 7645--7647
[]\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
[3088] [3089] [3090] [3091] [3092] [3093]
Underfull \hbox (badness 1642) in paragraph at lines 8037--8059
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3094] [3095]
Underfull \hbox (badness 10000) in paragraph at lines 8157--8174
[][][]\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 8157--8174
[][]\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 8200--8200
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 
Underfull \hbox (badness 1642) in paragraph at lines 8209--8231
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3096] [3097] [3098] [3099] [3100]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 
Underfull \hbox (badness 10000) in paragraph at lines 8520--8522
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3101]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558
 []\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.8565 \aliasA{sigma}{lmeObject}{sigma}
                                        [3102] [3103] [3104]
Underfull \hbox (badness 10000) in paragraph at lines 8726--8738
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113]
Underfull \hbox (badness 10000) in paragraph at lines 9317--9324
[][][]\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 9328--9328
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3114]
Underfull \hbox (badness 6300) in paragraph at lines 9410--9413
[]\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
[3115] [3116] [3117] [3118]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9679 ...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.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3119]
Underfull \hbox (badness 10000) in paragraph at lines 9699--9702
[]\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 9743--9746
[]\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 9743--9746
\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
[3120] [3121] [3122]
Underfull \hbox (badness 2435) in paragraph at lines 9917--9922
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 7291) in paragraph at lines 10207--10209
[]\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
[3128] [3129] [3130]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3131]
Underfull \hbox (badness 1596) in paragraph at lines 10452--10478
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3132] [3133] [3134]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3135] [3136]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 
Underfull \hbox (badness 2213) in paragraph at lines 10790--10795
[]\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[][][]
[3137]
Underfull \hbox (badness 10000) in paragraph at lines 10812--10816
[]\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
Underfull \hbox (badness 10000) in paragraph at lines 10831--10833
[]\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 10867--10867
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3138] [3139] [3140] [3141]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3142] [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152]
[3153]
Underfull \hbox (badness 6268) in paragraph at lines 11902--11912
[][][]\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 ,
[3154] [3155] [3156] [3157]
Underfull \hbox (badness 10000) in paragraph at lines 12163--12169
[][][]\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 ,
[3158] [3159] [3160] [3161] [3162]
Underfull \hbox (badness 6876) in paragraph at lines 12485--12487
[]\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
[3163] [3164]
Underfull \hbox (badness 2452) in paragraph at lines 12641--12648
[][][]\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 ,
[3165]
Underfull \hbox (badness 10000) in paragraph at lines 12706--12712
[][][]\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 ,
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176]
[3177] [3178] [3179]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3180]
Underfull \hbox (badness 10000) in paragraph at lines 13685--13688
[]\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
Underfull \hbox (badness 6016) in paragraph at lines 13713--13716
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.
Underfull \hbox (badness 2653) in paragraph at lines 13713--13716
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 1975) in paragraph at lines 13720--13723
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot
Underfull \hbox (badness 1838) in paragraph at lines 13728--13735
[]\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 13728--13735
\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
[3181]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
Underfull \hbox (badness 10000) in paragraph at lines 13792--13795
[]\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 13792--13795
\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
[3182]
Underfull \hbox (badness 4582) in paragraph at lines 13820--13823
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is
Underfull \hbox (badness 2418) in paragraph at lines 13820--13823
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and
Underfull \hbox (badness 2990) in paragraph at lines 13824--13827
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3183]
Underfull \hbox (badness 10000) in paragraph at lines 13900--13903
[]\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
Underfull \hbox (badness 1472) in paragraph at lines 13925--13932
\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 ,
[3184]
Underfull \hbox (badness 10000) in paragraph at lines 13994--13996
[][][]\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 ,
[3185] [3186] [3187] [3188]
Underfull \hbox (badness 1540) in paragraph at lines 14209--14214
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an
Underfull \hbox (badness 1215) in paragraph at lines 14256--14258
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3189] [3190] [3191] [3192] [3193]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202]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.15153 ...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.15153 ...Extract Random Effects}{random.effects}
                                                   [3203] [3204] [3205]
[3206] [3207] [3208] [3209] [3210] [3211] [3212]
Underfull \hbox (badness 1009) in paragraph at lines 15810--15819
\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
[3213] [3214] [3215]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3216] [3217] [3218] [3219]
Underfull \hbox (badness 10000) in paragraph at lines 16235--16253
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form
Underfull \hbox (badness 1708) in paragraph at lines 16235--16253
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3220]
Underfull \hbox (badness 10000) in paragraph at lines 16292--16298
[][][]\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 ,
[3221]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3222] [3223] [3224] [3225] [3226] [3227] [3228]
Underfull \hbox (badness 1728) in paragraph at lines 16812--16815
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3229] [3230] [3231] [3232] [3233]
Underfull \hbox (badness 1867) in paragraph at lines 17147--17156
\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 17147--17156
\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"
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17147--17156
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3234]
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for
Underfull \hbox (badness 10000) in paragraph at lines 17211--17219
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3235] [3236] [3237] [3238]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17465
[][][]\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 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 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3239] [3240] [3241] [3242] [3243] [3244] [3245] [3246]
Underfull \hbox (badness 10000) in paragraph at lines 17993--18003
[][][]\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 17993--18003
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18031--18036
\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
[3247]
Underfull \hbox (badness 3579) in paragraph at lines 18095--18100
\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
[3248]
Underfull \hbox (badness 3579) in paragraph at lines 18158--18163
\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
[3249]
Underfull \hbox (badness 1577) in paragraph at lines 18219--18221
[]\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 18221--18226
\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
[3250]
Underfull \hbox (badness 3579) in paragraph at lines 18284--18289
\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
[3251]
Underfull \hbox (badness 10000) in paragraph at lines 18317--18326
[][][]\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 18317--18326
[][]\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 ,
Underfull \hbox (badness 3579) in paragraph at lines 18356--18361
\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
[3252] [3253] [3254]
Underfull \hbox (badness 1009) in paragraph at lines 18505--18514
\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
[3255] [3256]
Underfull \hbox (badness 1009) in paragraph at lines 18639--18648
\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
[3257] [3258] [3259] [3260] [3261] [3262] [3263] [3264]) (./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}
                                                   [3265]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3266] [3267] [3268]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3269]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\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 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3270]
Underfull \hbox (badness 4013) in paragraph at lines 474--477
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3271]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3272]) (./rpart-pkg.tex
Chapter 27.
[3273] [3274] [3275] [3276]
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, ...)[] 
[3277]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3278] [3279] [3280]
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
[3281] [3282]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3283]
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[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3284]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3285]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3286] [3287] [3288]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\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 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method
Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y
Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3289]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\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
[3290]
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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 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3291] [3292] [3293] [3294] [3295] [3296]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\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 ',
[3297] [3298]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3299] [3300] [3301]) (./spatial-pkg.tex [3302]
Chapter 28.
[3303] [3304] [3305] [3306] [3307] [3308]
Underfull \hbox (badness 10000) in paragraph at lines 423--427
[3309] [3310] [3311] [3312] [3313] [3314] [3315] [3316] [3317] [3318] [3319]
[3320] [3321]) (./survival-pkg.tex [3322]
Chapter 29.
[3323] [3324]
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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.[] 
[3325] [3326]
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 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 
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 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.319 ... 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.319 ... Myelogenous Leukemia survival data}{aml}
                                                   [3327] [3328]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 416--416
 []\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 418--418
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3329]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3330] [3331]
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 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 
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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3333] [3334]
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 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3335] [3336] [3337]
Underfull \hbox (badness 1097) in paragraph at lines 968--970
[]\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 988--988
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3338] [3339]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3340]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1171 ...erapy for Stage B/C colon cancer}{colon}
                                                  
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[3342] [3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3347] [3348] [3349] [3350] [3351]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1988--1988
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3352] [3353] [3354]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2237--2237
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3355] [3356] [3357] [3358] [3359]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2554--2554
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
Underfull \hbox (badness 1389) in paragraph at lines 2567--2569
[]\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
[3360]
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[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3361]
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 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3362] [3363] [3364] [3365]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2945--2945
 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3366] [3367] [3368] [3369]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3211--3211
 []                    \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 )))[] 
[3370] [3371] [3372] [3373]
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[3375] [3376]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3620--3620
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3377] [3378]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3809--3809
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3379] [3380]
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 []\T1/pcr/m/n/9 mresid <- (lung$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[] 
[3381]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3382] [3383] [3384]
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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
[3385] [3386]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4297--4297
 []\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, ...)[] 
[3387] [3388]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3389]
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[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 
[3390]
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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)) +[] 
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4587--4587
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3391] [3392]
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 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3393]
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[3395] [3396]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \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/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,
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\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3397] [3398] [3399] [3400]
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 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 
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 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3401]
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 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3402] [3403] [3404] [3405] [3406]
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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,[] 
[3407] [3408] [3409] [3410]
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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 ),[] 
[3411] [3412] [3413] [3414]
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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
[3415]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 
[3416]
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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/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3417]
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3418]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3419] [3420] [3421]
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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 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3422] [3423] [3424]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3425]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3426] [3427]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3428] [3429] [3430] [3431]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3432]
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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
[3433] [3434]
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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
[3435]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3436] [3437] [3438]
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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 )[] 
[3439] [3440]
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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 )[] 
[3441] [3442] [3443] [3444]
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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)[] 
[3445] [3446] [3447] [3448]
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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 , 
[3472] [3473] [3474] [3475] [3476]
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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 , 
[3477] [3478]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3479] [3480] [3481] [3482] [3483] [3484] [3485]
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[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 
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[3487]
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This is `epsf.tex' v2.7.4 <14 February 2011>
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[5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17]
Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
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[40] [41]
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@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
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[42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] )
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
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[-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4]
[5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17]
Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]
[40] [41]
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@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi
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}] [2] [-1] Chapter 1 [1] Chapter 2 [2]
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[7] [8] [9] [10] [11] Chapter 3 [12] [13]
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TIONS[] @textrm to the value
[14] [15] [16] [17] Chapter 4 [18] [19]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29]
Chapter 7 [30] [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37]
Appendix A [38] [39]
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 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
[53] Appendix C [54] [55] [56] [57] [58] [59] [60]
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ig:/usr/lib/pkgconfig[] 
[61] [62]
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me/bin/javah[] 
[63] [64] [65] [66] [67] [68] [69] Appendix D [70] [71] [72]
(Function and variable index) [73] (Concept index) [74]
(Environment variable index) [75] [76] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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This is `epsf.tex' v2.7.4 <14 February 2011>
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[12] [13]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29]
Chapter 7 [30] [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37]
Appendix A [38] [39]
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[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
[53] Appendix C [54] [55] [56] [57] [58] [59] [60]
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[63] [64] [65] [66] [67] [68] [69] Appendix D [70] [71] [72]
(Function and variable index) [73] (./R-admin.vrs) (Concept index) [74]
(./R-admin.cps) (Environment variable index) [75] (./R-admin.ens) [76] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3
[12] [13]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29]
Chapter 7 [30] [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37]
Appendix A [38] [39]
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[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
[53] Appendix C [54] [55] [56] [57] [58] [59] [60]
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[63] [64] [65] [66] [67] [68] [69] Appendix D [70] [71] [72]
(Function and variable index) [73] (./R-admin.vrs) (Concept index) [74]
(./R-admin.cps) (Environment variable index) [75] (./R-admin.ens) [76] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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[12] [13]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29]
Chapter 7 [30] [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37]
Appendix A [38] [39]
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[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
[53] Appendix C [54] [55] [56] [57] [58] [59] [60]
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 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 
[61] [62]
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 []@texttt JAVAH=/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Ho
me/bin/javah[] 
[63] [64] [65] [66] [67] [68] [69] Appendix D [70] [71] [72]
(Function and variable index) [73] (./R-admin.vrs) (Concept index) [74]
(./R-admin.cps) (Environment variable index) [75] (./R-admin.ens) [76] )
(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>
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] (Acknowledgements)
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 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2]
[3] [4] 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] (Concept index) [29] [30] )
(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
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e/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
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entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc)
(Acknowledgements)
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 [][]@textbf dataframes2xls[][]| 
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 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] [2] [3] [4] 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] (./R-data.vrs [29]) (Concept index) [30]
(./R-data.cps) [31] )
(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/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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fonts/type1/public/amsfonts/cm/cmtt9.pfb>
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entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc)
(Acknowledgements)
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 [][]@textbf dataframes2xls[][]| 
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 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] [2] [3] [4] 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] (./R-data.vrs [29]) (Concept index) [30]
(./R-data.cps) [31] )
(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
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cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
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entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc)
(Acknowledgements)
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 [][]@textbf dataframes2xls[][]| 
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 [][]@textbf RPostgreSQL[][]| 
Chapter 1 [1] [2] [3] [4] 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] (./R-data.vrs [29]) (Concept index) [30]
(./R-data.cps) [31] )
(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
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sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
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) localization, formatting, and turning on texinfo input format.)
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(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] (Acknowledgements) Chapter 1 [1]
Cross reference values unknown; you must run TeX again. [2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 495--498
[]@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] [18] [19] [20] [21]
[22] [23] [24]
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 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
[25]
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 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[26] [27]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[28] [29]
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 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]
[45] [46] [47] [48] [49] [50] [51]
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 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
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 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
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 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
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 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[52] [53] [54] [55] [56] [57] [58]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[59] [60] [61] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71]
[72] [73] [74] [75]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[76] [77]
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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
[78] [79] [80] [81] Chapter 3 [82] [83] [84] [85] [86] [87] [88] [89]
Chapter 4 [90] [91] [92] [93] [94]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[95] [96] [97]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[98] [99]
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 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[100]
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 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[101] [102] [103] [104] Chapter 5 [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[115] [116] [117] [118] [119] [120]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[121] [122] [123] [124] [125] [126] [127] [128] [129] [130]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
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 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[143] [144] Chapter 6 [145] [146] [147] [148] [149] [150] [151] [152] [153]
[154] [155] [156] [157] Warning: unbalanced parentheses in @def... [158]
[159] [160] [161] [162] [163]
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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 [164] [165] Chapter 8 [166] [167] [168]
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 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[169]
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 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[170] [171] [172] [173] [174] [175]
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 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[176] [177] (Function and variable index) [178] (Concept index) [179] [180] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
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pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></us
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Output written on R-exts.pdf (183 pages, 889103 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-exts.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc)
(Acknowledgements) Chapter 1 [1] [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] [18] [19] [20] [21]
[22] [23] [24]
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 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
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 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[25] [26] [27]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[28] [29]
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 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]
[45] [46] [47] [48] [49] [50] [51]
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 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
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 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
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 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
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 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[52] [53] [54] [55] [56] [57] [58]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[59] [60] [61] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71]
[72] [73] [74] [75]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[76] [77]
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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
[78] [79] [80] [81] Chapter 3 [82] [83] [84] [85] [86] [87] [88] [89]
Chapter 4 [90] [91] [92] [93] [94]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[95] [96] [97]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[98]
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 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
[99]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[100]
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 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[101] [102] [103] [104] Chapter 5 [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[115] [116] [117] [118] [119] [120]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[121] [122] [123] [124] [125] [126] [127] [128] [129] [130]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
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 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[143] [144] Chapter 6 [145] [146] [147] [148] [149] [150] [151] [152] [153]
[154] [155] [156] [157] Warning: unbalanced parentheses in @def... [158]
[159] [160] [161] [162]
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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_
[163] Chapter 7 [164] [165] Chapter 8 [166] [167] [168]
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 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[169]
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 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[170] [171] [172] [173] [174] [175]
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 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[176] [177] (Function and variable index) [178] (./R-exts.vrs [179] [180])
(Concept index) [181] (./R-exts.cps [182]) [183] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
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cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
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/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/sha
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0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
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Output written on R-exts.pdf (189 pages, 952555 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-exts.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc)
(Acknowledgements) Chapter 1 [1] [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] [18] [19] [20] [21]
[22] [23] [24]
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 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
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 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[25] [26] [27]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[28] [29]
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 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]
[45] [46] [47] [48] [49] [50] [51]
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 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
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 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
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 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
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 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[52] [53] [54] [55] [56] [57] [58]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[59] [60] [61] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71]
[72] [73] [74] [75]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[76] [77]
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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
[78] [79] [80] [81] Chapter 3 [82] [83] [84] [85] [86] [87] [88] [89]
Chapter 4 [90] [91] [92] [93] [94]
Underfull \hbox (badness 10000) in paragraph at lines 8206--8215
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[95] [96] [97]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[98]
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 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 
[99]
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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -
[100]
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 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[101] [102] [103] [104] Chapter 5 [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[115] [116] [117] [118] [119] [120]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[121] [122] [123] [124] [125] [126] [127] [128] [129] [130]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
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 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[143] [144] Chapter 6 [145] [146] [147] [148] [149] [150] [151] [152] [153]
[154] [155] [156] [157] Warning: unbalanced parentheses in @def... [158]
[159] [160] [161] [162]
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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_
[163] Chapter 7 [164] [165] Chapter 8 [166] [167] [168]
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 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[169]
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 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[170] [171] [172] [173] [174] [175]
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 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[176] [177] (Function and variable index) [178] (./R-exts.vrs [179] [180])
(Concept index) [181] (./R-exts.cps [182]) [183] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/cm-super/cm-super-t1.enc}</usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
9.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/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/
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1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/cm-super/sfrm1095.pfb>
Output written on R-exts.pdf (189 pages, 952502 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 restricted \write18 enabled.
entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-exts.aux
) (./R-defs.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc)
(Acknowledgements) Chapter 1 [1] [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] [18] [19] [20] [21]
[22] [23] [24]
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pp model/*/*.cpp model/*/*/*.cpp)[] 
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 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[25] [26] [27]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[28] [29]
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 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]
[45] [46] [47] [48] [49] [50] [51]
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 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 
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 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 
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 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 
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 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[52] [53] [54] [55] [56] [57] [58]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[59] [60] [61] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71]
[72] [73] [74] [75]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[76] [77]
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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
[78] [79] [80] [81] Chapter 3 [82] [83] [84] [85] [86] [87] [88] [89]
Chapter 4 [90] [91] [92] [93] [94]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[95] [96] [97]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[98]
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odr_violation=0'[] 
[99]
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exttt -
[100]
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 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[101] [102] [103] [104] Chapter 5 [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[115] [116] [117] [118] [119] [120]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[121] [122] [123] [124] [125] [126] [127] [128] [129] [130]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
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 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[143] [144] Chapter 6 [145] [146] [147] [148] [149] [150] [151] [152] [153]
[154] [155] [156] [157] Warning: unbalanced parentheses in @def... [158]
[159] [160] [161] [162]
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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_
[163] Chapter 7 [164] [165] Chapter 8 [166] [167] [168]
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 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[169]
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 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[170] [171] [172] [173] [174] [175]
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 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[176] [177] (Function and variable index) [178] (./R-exts.vrs [179] [180])
(Concept index) [181] (./R-exts.cps [182]) [183] )
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cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb><
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
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}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again.
Chapter 1 [1] [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] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.pdf>
[35] [36] <./images/ice.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] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72] [73]
[74] [75] Chapter 13 [76] [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] Appendix E [94] Appendix F [95]
[96] )
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
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}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc)
(Preface) Chapter 1 [1] [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] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p
df> [35] [36] <./images/ice.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] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72]
[73] [74] [75] Chapter 13 [76] [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] (./R-intro.vrs [94] [95]) Appendix E
[96] (./R-intro.cps [97]) Appendix F [98] [99] )
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ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
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defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
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}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc)
(Preface) Chapter 1 [1] [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] <./images/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.p
df> [35] [36] <./images/ice.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] <./images/fig11.pdf> [71] <./images/fig12.pdf> [72]
[73] [74] [75] Chapter 13 [76] [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] (./R-intro.vrs [94] [95]) Appendix E
[96] (./R-intro.cps [97]) Appendix F [98] [99] )
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[13] [14] [15]
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 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 
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 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 
Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "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]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
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@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link, as
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
Underfull \hbox (badness 10000) in paragraph at lines 3852--3857
 @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] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11
[56] Chapter 12 [57] [58] (Function and variable index) [59] (Concept index)
[60] [61] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
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Output written on R-ints.pdf (64 pages, 400397 bytes).
Transcript written on R-ints.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-ints.aux
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}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 
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 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 
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 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 
Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "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]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link, as
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
Underfull \hbox (badness 10000) in paragraph at lines 3852--3857
 @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] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11
[56] Chapter 12 [57] [58] (Function and variable index) [59] (./R-ints.vrs
[60]) (Concept index) [61] (./R-ints.cps) [62] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
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Output written on R-ints.pdf (66 pages, 450230 bytes).
Transcript written on R-ints.log.
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entering extended mode
(/builddir/build/BUILD/R-3.5.0/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/texinfo.tex
Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-ints.aux
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}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15]
Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 
Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 
Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 
Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
ly,
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link, as
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
Underfull \hbox (badness 10000) in paragraph at lines 3852--3857
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11
[56] Chapter 12 [57] [58] (Function and variable index) [59] (./R-ints.vrs
[60]) (Concept index) [61] (./R-ints.cps) [62] )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type
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Output written on R-ints.pdf (66 pages, 450228 bytes).
Transcript written on R-ints.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi
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(./version.texi) [1{/usr/share/texlive/texmf/fonts/map/pdftex/updmap/pdftex.map
}] [2] [-1] Chapter 1 Chapter 2 [1] [2]
Cross reference values unknown; you must run TeX again.
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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 4342--4344
[]@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] (Concept Index)
[52] Appendix A [53] [54] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
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(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
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}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1
Chapter 2 [1] [2]
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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]
Underfull \hbox (badness 10000) in paragraph at lines 4342--4344
[]@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] (./R-lang.vrs
[52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
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defuns, macros, cross references, insertions, (./epsf.tex
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Chapter 2 [1] [2]
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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] (./R-lang.vrs
[52]) (Concept Index) [53] (./R-lang.cps) Appendix A [54] [55] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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Loading texinfo [version 2013-02-01.11]: pdf, fonts, markup, glyphs,
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defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-lang.aux
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(/usr/share/texlive/texmf-local/texmf-compat/tex/texinfo/txi-en.tex))
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}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1
Chapter 2 [1] [2]
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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] (./R-lang.vrs
[52]) (Concept Index) [53] (./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
-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (60 pages, 376046 bytes).
Transcript written on R-lang.log.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
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+ make MAKEINFO=texi2any info
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texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi
texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi
R-exts.texi:10008: warning: `.' or `,' must follow @xref, not f
texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi
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+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
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+ mv doc/manual/R-intro.info.utf8 doc/manual/R-intro.info
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-FAQ.info.utf8 doc/manual/R-FAQ.info
+ mv doc/manual/R-FAQ.info.utf8 doc/manual/R-FAQ.info
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/FAQ.utf8 doc/FAQ
+ mv doc/FAQ.utf8 doc/FAQ
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-admin.info.utf8 doc/manual/R-admin.info
+ mv doc/manual/R-admin.info.utf8 doc/manual/R-admin.info
+ for i in doc/manual/R-intro.info doc/manual/R-FAQ.info doc/FAQ doc/manual/R-admin.info doc/manual/R-exts.info-1
+ iconv -f iso-8859-1 -t utf-8 -o doc/manual/R-exts.info-1.utf8 doc/manual/R-exts.info-1
+ mv doc/manual/R-exts.info-1.utf8 doc/manual/R-exts.info-1
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Xmbwav
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64
++ dirname /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64
+ cd R-3.5.0
+ make DESTDIR=/builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64 install install-info
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R
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make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/doc'
installing doc ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/man/man1
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installing doc/manual ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0/manual
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0/manual/images
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mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/etc
installing etc ...
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installing share ...
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/R
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/dictionaries
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/encodings
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/java
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/licenses
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/make
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/Rd
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/Rd/macros
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/sh
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/texmf
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/texmf/bibtex/bib
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/texmf/bibtex/bst
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/texmf/tex/latex
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mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/bin
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin
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mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/include/R
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mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/lib
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make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra/tzone'
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make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra/xdr'
make[3]: Nothing to be done for `install'.
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make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/extra/intl'
make[3]: Nothing to be done for `install'.
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make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/extra'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/appl'
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make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/appl'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/nmath'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/nmath'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/unix'
gcc -m64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mcpu=power7 -mtune=power7  -Wl,-z,relro  -DR_HOME='"/usr/lib64/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/pkgconfig
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/unix'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/exec
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/main'
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make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/main'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/internet'
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/modules
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/internet'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
make[3]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules/lapack'
make[3]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/modules/X11'
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make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/modules'
make[2]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/library'
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/library'
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src'
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/tests'
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make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
mkdir -p -- /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/info
/usr/bin/install -c -m 644 "./dir" "/builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/info"
installing R info pages ...
updating '/usr/share/info/dir' ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
+ make DESTDIR=/builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64 install-pdf
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/doc/manual'
+ rm -f /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/info/dir
+ rm -f /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/info/dir.old
+ mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0
+ install -p CAPABILITIES /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0
+ cd src/nmath/standalone
+ make install DESTDIR=/builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64
make[1]: Entering directory `/builddir/build/BUILD/R-3.5.0/src/include'
make[1]: `Rmath.h' is up to date.
make[1]: Leaving directory `/builddir/build/BUILD/R-3.5.0/src/include'
+ mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/etc/ld.so.conf.d
+ echo /usr/lib64/R/lib
+ mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/library
+ mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib/rpm/macros.d/
+ install -m0644 /builddir/build/SOURCES/macros.R /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib/rpm/macros.d/
+ mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib/rpm/
+ install -m0755 /builddir/build/SOURCES/R-make-search-index.sh /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib/rpm/
+ touch -r README /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0/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-3.5.0-1.el7.ppc64/usr/bin/R
+ sed -i 's|\..\/\..|/usr/lib64/R|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0/html/packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/bkde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/bkde2D.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/bkfe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/dpih.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/dpik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/dpill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/KernSmooth/html/locpoly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Aids2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Animals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Boston.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Cars93.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Cushings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/DDT.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/GAGurine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Insurance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/MASS-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Null.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/OME.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Pima.tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Rabbit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Rubber.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/SP500.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Sitka.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Sitka89.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Skye.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/Traffic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/UScereal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/UScrime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/VA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/abbey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/accdeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/addterm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/anorexia.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/anova.negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/area.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/bacteria.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/bandwidth.nrd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/bcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/beav1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/beav2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/biopsy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/birthwt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/boxcox.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/cabbages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/caith.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/cats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/cement.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/chem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/con2tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/confint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/contr.sdif.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/coop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/corresp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/cov.rob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/cov.trob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/cpus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/crabs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/deaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/denumerate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/dose.p.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/drivers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/dropterm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/eagles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/epil.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/eqscplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/farms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/fgl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/fitdistr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/forbes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/fractions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/galaxies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/gamma.dispersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/gamma.shape.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/gehan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/genotype.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/geyser.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/gilgais.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/ginv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/glm.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/glm.nb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/glmmPQL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/hills.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/hist.scott.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/housing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/huber.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/hubers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/immer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/isoMDS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/kde2d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/ldahist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/leuk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/lm.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/lm.ridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/loglm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/loglm1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/logtrans.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/lqs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/mammals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/mcycle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/menarche.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/michelson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/minn38.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/motors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/muscle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/mvrnorm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/negative.binomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/newcomb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/nlschools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/npk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/npr1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/oats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/painters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/pairs.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/parcoord.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/petrol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/phones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/plot.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/plot.mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/plot.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/polr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/predict.glmmPQL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/predict.lda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/predict.lqs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/predict.mca.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/predict.qda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/profile.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/qda.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/quine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/rational.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/renumerate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/rlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/rms.curv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/rnegbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/road.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/rotifer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/sammon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/ships.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/shoes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/shrimp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/shuttle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/snails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/stdres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/steam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/stepAIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/stormer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/studres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/summary.loglm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/summary.negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/summary.rlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/survey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/synth.tr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/html/theta.md.html
+ for i in '$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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
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+ for i in '$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'
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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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
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+ for i in '$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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/dsparseMatrix-class.html
+ for i in '$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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/externalFormats.html
+ for i in '$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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
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+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/indMatrix-class.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-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/isTriangular.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/kronecker-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/ldenseMatrix-class.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'
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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-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/nMatrix-class.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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/norm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/nsparseMatrix-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/nsyMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/ntrMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/number-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/pMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/printSpMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/qr-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/rankMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/rcond.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/rep2abI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/replValue-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/rleDiff-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/rsparsematrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/solve-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/spMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/sparse.model.matrix.html
+ for i in '$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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/sparseQR-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/sparseVector-class.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-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/symmetricMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/symmpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/triangularMatrix-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/uniqTsparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/unpack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/unused-classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/Matrix/html/updown.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Arithmetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/AsIs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Bessel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/CallExternal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Colon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Comparison.html
+ for i in '$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-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Cstack_info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/DateTimeClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Dates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Encoding.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/EnvVar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Extract.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Extract.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Extract.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Extremes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Foreign-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Foreign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Hyperbolic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ISOdatetime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/InternalMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/La_library.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/La_version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Last.value.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Log.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Logic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/LongVectors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/MathFun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Memory-limits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Memory.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/NA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/NULL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/NumericConstants.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Ops.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Paren.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Platform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Primitive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Quotes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Random-user.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Random.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/RdUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Recall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Reserved.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Rhome.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Round.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Signals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Special.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Startup.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Syntax.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.getenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.getpid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.glob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.localeconv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.readlink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.setFileTime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.setenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.sleep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Sys.which.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Trig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/UseMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Vectorize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/Version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/abbreviate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/agrep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/all.equal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/all.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/allnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/any.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/aperm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/append.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/apply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/args.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/as.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/as.POSIXlt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/as.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/as.environment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/as.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/assign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/assignOps.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/attach.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/attr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/attributes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/autoload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/backsolve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/base-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/base-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/base-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/base-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/basename.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/bincode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/bindenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/bitwise.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/body.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/bquote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/browser.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/browserText.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/builtins.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/by.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/c.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/callCC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/capabilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/cat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/cbind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/char.expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/character.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/charmatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/chartr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/chkDots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/chol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/chol2inv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/col.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/colSums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/colnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/commandArgs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/comment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/complex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/conditions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/conflicts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/connections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/contributors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/copyright.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/crossprod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/cumsum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/curlGetHeaders.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/cut.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/cut.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/data.class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/data.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dataframeHelpers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dcf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/debug.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/delayedAssign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/deparse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/deparseOpts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/det.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/detach.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/diff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/difftime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dimnames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/do.call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dontCheck.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/double.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dput.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/drop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/droplevels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dump.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/duplicated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/dynload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/eapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/eigen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/encodeString.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/environment.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/eval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/exists.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/expand.grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/expression.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/extSoftVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/file.access.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/file.choose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/file.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/file.path.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/file.show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/files2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/find.package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/findInterval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/force.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/forceAndCall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/formals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/format.info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/format.pval.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/formatDL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/formatc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/funprog.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/gc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/gc.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/gctorture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/getCallingDLL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/getDLLRegisteredRoutines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/getLoadedDLLs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/getNativeSymbolInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/gettext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/getwd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/gl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/grep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/grepRaw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/groupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/grouping.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/gzcon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/hexmode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/iconv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/icuSetCollate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/identical.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/identity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ifelse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/integer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/interaction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/interactive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/invisible.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.finite.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.language.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.recursive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.single.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/is.unsorted.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/isR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/isS4.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/isSymmetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/jitter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/kappa.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/kronecker.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/l10n_info.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/labels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/lapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/lazyload.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/length.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/lengths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/levels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/libPaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/libcurlVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/library.dynam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/library.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/license.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/list.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/list2env.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/load.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/locales.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/logical.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/lower.tri.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/make.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/make.unique.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/mapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/margin.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/mat.or.vec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/match.arg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/match.call.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/match.fun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/match.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/matmult.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/maxCol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/mean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/memCompress.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/memory.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/merge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/message.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/missing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/mode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/name.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/nargs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/nchar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/nlevels.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/noquote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/norm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/normalizePath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/notyet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/nrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ns-dblcolon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ns-hooks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ns-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ns-load.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ns-reflect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/ns-topenv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/numeric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/numeric_version.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/octmode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/on.exit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/order.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/outer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/parse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/paste.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/path.expand.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/pcre_config.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/pmatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/polyroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/pos.to.env.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/pretty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/print.dataframe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/print.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/print.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/prmatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/proc.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/prod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/prop.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/pushBack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/qr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/qraux.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/quit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/range.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/raw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rawConnection.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rawConversion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/readBin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/readChar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/readLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/readRDS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/readRenviron.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/readline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/reg.finalizer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/regex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/regmatches.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/replace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/round.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/row.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/row.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/rowsum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sQuote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sample.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/save.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/scale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/scan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/search.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/seek.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/seq.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/seq.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/seq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sequence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/serialize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/setTimeLimit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/shQuote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/showConnections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/slice.index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/slotOp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/socketSelect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/solve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sort.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/source.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/split.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sprintf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/srcfile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/standardGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/startsWith.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/stop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/stopifnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/strptime.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/strrep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/strsplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/strtoi.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/strtrim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/structure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/strwrap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/subset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/substitute.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/substr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/summary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/svd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sweep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/switch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sys.parent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/sys.source.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/system.file.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/system.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/system.time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/system2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/t.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/tabulate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/tapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/taskCallback.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/taskCallbackManager.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/taskCallbackNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/tempfile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/textconnections.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/tilde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/timezones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/toString.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/trace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/traceback.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/tracemem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/transform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/trimws.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/try.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/typeof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/unique.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/unlink.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/unlist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/unname.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/userhooks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/utf8Conversion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/validUTF8.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/vector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/warning.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/warnings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/weekday.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/which.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/which.min.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/with.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/withVisible.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/write.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/writeLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/xtfrm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/zMachine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/zScript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/zapsmall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/zpackages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/base/html/zutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/EEF.profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/Imp.Estimates.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/abc.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/acme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/aids.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/aircondit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/amis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/aml.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/beaver.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/bigcity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/boot-practicals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/boot.array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/boot.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/brambles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/breslow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/calcium.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cane.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/capability.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/catsM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cav.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cd4.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cd4.nested.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/censboot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/channing.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/claridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cloth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/co.transfer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/coal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/corr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cum3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/cv.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/darwin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/dogs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/downs.bc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/ducks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/empinf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/envelope.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/exp.tilt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/fir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/freq.array.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/frets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/glm.diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/glm.diag.plots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/gravity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/hirose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/imp.weights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/inv.logit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/islay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/jack.after.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/k3.linear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/linear.approx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/lines.saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/logit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/manaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/motor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/neuro.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/nitrofen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/nodal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/norm.ci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/nuclear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/paulsen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/plot.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/poisons.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/polar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/print.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/print.bootci.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/print.saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/print.simplex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/remission.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/saddle.distn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/saddle.distn.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/saddle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/salinity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/simplex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/simplex.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/smooth.f.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/sunspot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/survival.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/tau.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/tilt.boot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/tsboot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/tuna.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/urine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/var.linear.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/boot/html/wool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/SOM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/batchSOM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/condense.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/knn.cv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/knn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/knn1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/lvq1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/lvq2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/lvq3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/lvqinit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/lvqtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/multiedit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/olvq1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/reduce.nn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/class/html/somgrid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/agnes.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/agriculture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/animals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/bannerplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/chorSub.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/clara.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/clusGap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/clusplot.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/clusplot.partition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/cluster-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/coef.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/daisy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/dissimilarity.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/ellipsoidhull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/fanny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/fanny.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/flower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/lower.to.upper.tri.inds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/mona.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/pam.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/partition.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/plantTraits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/plot.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/plot.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/plot.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/plot.partition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/pltree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/pluton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/predict.ellipsoid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.dissimilarity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.fanny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/print.pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/ruspini.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/silhouette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/sizeDiss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/summary.agnes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/summary.clara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/summary.diana.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/summary.mona.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/summary.pam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/twins.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/volume.ellipsoid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/votes.repub.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/cluster/html/xclara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/codetools/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/codetools/html/checkUsage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/codetools/html/codetools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/codetools/html/findGlobals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/codetools/html/showTree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/compiler/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/compiler/html/compile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/AirPassengers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/BJsales.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/BOD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/ChickWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/DNase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/EuStockMarkets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Formaldehyde.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/HairEyeColor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Harman23.cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Harman74.cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Indometh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/InsectSprays.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/JohnsonJohnson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/LakeHuron.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/LifeCycleSavings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Loblolly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Nile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Orange.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/OrchardSprays.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/PlantGrowth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Puromycin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Theoph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/Titanic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/ToothGrowth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/UCBAdmissions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/UKDriverDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/UKLungDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/UKgas.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/USAccDeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/USArrests.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/USJudgeRatings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/USPersonalExpenditure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/VADeaths.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/WWWusage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/WorldPhones.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/ability.cov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/airmiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/airquality.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/anscombe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/attenu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/attitude.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/austres.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/beavers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/cars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/chickwts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/co2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/crimtab.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/datasets-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/discoveries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/esoph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/euro.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/eurodist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/faithful.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/freeny.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/infert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/iris.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/islands.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/lh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/longley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/lynx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/morley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/mtcars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/nhtemp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/nottem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/npk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/occupationalStatus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/precip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/presidents.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/pressure.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/quakes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/randu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/rivers.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/rock.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/sleep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/stackloss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/state.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/sunspot.month.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/sunspot.year.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/sunspots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/swiss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/treering.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/trees.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/uspop.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/volcano.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/warpbreaks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/women.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/datasets/html/zCO2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/lookup.xport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.S.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.arff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.dbf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.dta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.epiinfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.mtp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.octave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.spss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.ssd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.systat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/read.xport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/write.arff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/write.dbf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/write.dta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/foreign/html/write.foreign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/Devices.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/Hershey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/Japanese.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/Type1Font.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/adjustcolor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/as.graphicsAnnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/as.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/axisTicks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/boxplot.stats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/cairo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/check.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/chull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/cm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/col2rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/colorRamp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/contourLines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/convertColor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/densCols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev.capabilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev.capture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev.flush.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev.interactive.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/dev2bitmap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/devAskNewPage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/embedFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/extendrange.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/getGraphicsEvent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/grDevices-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/grSoftVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/gray.colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/gray.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/hcl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/hsv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/make.rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/n2mfrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/nclass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/palette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/palettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/pdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/pdf.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/pictex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/plotmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/png.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/postscript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/postscriptFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/pretty.Date.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/ps.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/quartz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/quartzFonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/recordGraphics.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/recordplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/rgb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/rgb2hsv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/savePlot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/trans3d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/x11.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/x11Fonts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/xfig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/xy.coords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/xyTable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grDevices/html/xyz.coords.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/abline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/arrows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/assocplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/axTicks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/axis.POSIXct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/axis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/barplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/box.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/boxplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/boxplot.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/bxp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/cdplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/clip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/contour.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/convertXY.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/coplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/curve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/dotchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/filled.contour.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/fourfoldplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/graphics-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/graphics-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/hist.POSIXt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/hist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/identify.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/image.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/legend.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/lines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/locator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/matplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/mosaicplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/mtext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/pairs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/panel.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/par.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/persp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/pie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.dataframe.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.design.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.window.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plot.xy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/plothistogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/points.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/polygon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/polypath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/rasterImage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/rect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/rug.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/screen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/segments.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/smoothScatter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/spineplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/stars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/stem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/stripchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/strwidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/sunflowerplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/symbols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/text.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/title.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/units.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/xspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/graphics/html/zAxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/Grid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/absolute.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/arrow.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/calcStringMetric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/current.viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/dataViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/depth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/drawDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/editDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/explode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/gEdit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/gPath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/getNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/gpar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.DLapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.add.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.bezier.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.cap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.circle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.clip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.copy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.curve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.delay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.display.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.draw.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.force.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.function.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.grab.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.grep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.grill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.grob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.lines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.locator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.move.to.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.newpage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.null.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.pack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.path.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.place.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.plot.and.legend.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.points.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.polygon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.pretty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.raster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.record.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.rect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.refresh.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.remove.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.reorder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.roundrect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.segments.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.set.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.show.layout.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.show.viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.text.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.xaxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.xspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grid.yaxis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grobName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grobWidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/grobX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/legendGrob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/makeContent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/plotViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/resolveRasterSize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/showGrob.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/showViewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/stringWidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/unit.c.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/unit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/unit.length.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/unit.pmin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/unit.rep.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/valid.just.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/validDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/viewport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/viewports.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/vpPath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/widthDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/xDetails.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/grid/html/xsplinePoints.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/Lattice.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/Rows.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/USMortality.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/axis.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/banking.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/barchart.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/barley.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/cloud.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/draw.colorkey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/draw.key.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/environmental.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/ethanol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/histogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/interaction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/lattice.options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/latticeParseFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/level.colors.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/levelplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/llines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/lset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/make.groups.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/melanoma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/oneway.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/packet.panel.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.axis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.barchart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.bwplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.cloud.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.densityplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.dotplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.functions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.histogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.levelplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.number.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.pairs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.parallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.qqmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.qqmathline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.smoothScatter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.stripplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.superpose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.violin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/panel.xyplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/prepanel.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/prepanel.functions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/print.trellis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/qq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/qqmath.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/rfs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/shingles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/simpleKey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/simpleTheme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/singer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/splom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/strip.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/tmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/trellis.device.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/trellis.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/trellis.par.get.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/update.trellis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/utilities.3d.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/xyplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/lattice/html/xyplot.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/BasicClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Classes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Classes_Details.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Documentation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/EmptyMethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/EnvironmentClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/GenericFunctions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Introduction.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/LanguageClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/LinearMethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/MethodDefinition-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/MethodSupport.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/MethodWithNext-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/MethodsList-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/MethodsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Methods_Details.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Methods_for_Nongenerics.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/Methods_for_S3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/NextMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/ObjectsWithPackage-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/RClassUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/RMethodUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/S3Part.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/S4groupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/SClassExtension-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/StructureClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/TraceClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/as.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/callGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/canCoerce.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/cbind2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/className.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/classRepresentation-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/classesToAM.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/dotsMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/evalSource.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/findClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/findMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/fixPrevious.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/genericFunction-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/getClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/getMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/getPackageName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/hasArg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/implicitGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/inheritedSlotNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/initialize-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/is.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/isSealedMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/languageEl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/localRefClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/method.skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/methodUtilities.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/methods-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/methods-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/methods-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/new.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/nonStructure-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/promptClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/promptMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/refClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/removeMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/representation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/selectSuperClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setAs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setClassUnion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setGroupGeneric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setIs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setLoadActions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setMethod.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setOldClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/setSClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/showMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/signature-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/slot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/stdRefClass.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/substituteDirect.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/testInheritedMethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/validObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/html/zBasicFunsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Beta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Predict.matrix.cr.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Predict.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Predict.matrix.soap.film.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Rrank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Sl.initial.repara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Sl.repara.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Sl.setup.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/Tweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/anova.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/bam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/bam.update.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/bandchol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/bug.reports.mgcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/cSplineDes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/choose.k.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/columb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/concurvity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/coxpht.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/dDeta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/exclude.too.far.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/extract.lme.cov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/family.mgcv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/fix.family.link.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/fixDependence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/formXtViX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/formula.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/fs.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/full.score.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.check.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.convergence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.fit3.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.fit5.post.proc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.models.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.outer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.reparam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.scale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.selection.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.side.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam.vcomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gam2objective.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gamObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gamSim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gamlss.etamu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gamlss.gH.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gamm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gaulss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/get.var.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/gevlss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/identifiability.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/in.out.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/inSide.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/influence.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/initial.sp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/interpret.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/jagam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/ldTweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/ldetS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/linear.functional.terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/logLik.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/ls.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/magic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/magic.post.proc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mgcv-FAQ.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mgcv-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mgcv-parallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mini.roots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/missing.data.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/model.matrix.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mono.con.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/mvn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/negbin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/new.name.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/notExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/notExp2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/null.space.dimension.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/ocat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/one.se.rule.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/pcls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/pdIdnot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/pdTens.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/pen.edf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/place.knots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/plot.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/polys.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/predict.bam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/predict.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/print.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/qq.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/rTweedie.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/random.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/residuals.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/rig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/rmvn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/s.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/scat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/sdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/single.index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/slanczos.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.ad.smooth.spec.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 '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.ds.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.fs.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.gp.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.mrf.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.re.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.so.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.sos.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.t2.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.tensor.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth.terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smooth2random.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/smoothCon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/sp.vcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/spasm.construct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/step.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/summary.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/t2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/te.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/tensor.prod.model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/totalPenaltySpace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/trichol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/trind.generator.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/uniquecombs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/vcov.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/vis.gam.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/ziP.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/html/ziplss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/ACF.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/ACF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/ACF.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Alfalfa.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Assay.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/BodyWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Cefamandole.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Covariate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Covariate.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Dialyzer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Dim.corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Dim.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Dim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Dim.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Earthquake.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Extract.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Fatigue.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Gasoline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Glucose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Glucose2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Gun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/IGF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Initialize.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Initialize.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Initialize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Initialize.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Initialize.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Initialize.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/LDEsysMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Machines.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/MathAchSchool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/MathAchieve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Matrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Meat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Milk.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Muscle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Names.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Names.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Names.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Names.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Nitrendipene.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Oats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Orthodont.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Ovary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Oxboys.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Oxide.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/PBG.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Phenobarb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Pixel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Quinidine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Rail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/RatPupWeight.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Relaxin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Remifentanil.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Soybean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Spruce.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Tetracycline1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Tetracycline2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/VarCorr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.corExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.corGaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.corLin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.corRatio.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.corSpher.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.default.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Variogram.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Wafer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Wheat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/Wheat2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/allCoef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/anova.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/anova.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/as.matrix.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/as.matrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/as.matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/asOneFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/asTable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/augPred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/balancedGrouped.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/bdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/coef.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/collapse.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/collapse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/comparePred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corAR1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corARMA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corCAR1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corCompSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corFactor.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corFactor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corGaus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corLin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corMatrix.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corMatrix.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corMatrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corNatural.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corRatio.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corSpatial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corSpher.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/corSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/ergoStool.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fdHess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fitted.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fitted.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fitted.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fitted.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fitted.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fitted.nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fixed.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/fixef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/formula.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/formula.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/formula.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getCovariate.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getCovariate.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getCovariate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getCovariate.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getCovariateFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getData.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getData.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getData.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroups.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getGroupsFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getResponse.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getResponseFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/getVarCov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gls-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/glsControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/glsObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gnlsControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gnlsObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/gsummary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/intervals.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/intervals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/intervals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/intervals.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/isBalanced.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/isInitialized.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lmList.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lme.groupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lme.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lmeControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lmeObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logDet.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logDet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logDet.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logDet.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/logLik.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/model.matrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/needUpdate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/needUpdate.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlme.nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlmeControl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlmeObject.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/nlsList.selfStart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pairs.compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pairs.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pairs.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdCompSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdConstruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdConstruct.pdBlocked.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdDiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdFactor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdFactor.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdIdent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdLogChol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdMatrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdMatrix.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdNatural.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pdSymm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/phenoModel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.ACF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.Variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.augPred.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.compareFits.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.intervals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.nffGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.nfnGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.nmGroupedData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.ranef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/plot.ranef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/pooledSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/predict.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/predict.gnls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/predict.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/predict.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/predict.nlme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/print.summary.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/print.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/qqnorm.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/qqnorm.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/quinModel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/random.effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/ranef.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/ranef.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/recalc.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/recalc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/recalc.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/recalc.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/recalc.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.gnlsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/residuals.nlmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/simulate.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/solve.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/solve.reStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/splitFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.corStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.lmList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.lme.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.nlsList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.pdMat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/summary.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/update.modelStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/update.varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varComb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varConstPower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varExp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varFixed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varFunc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varIdent.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varPower.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varWeights.glsStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varWeights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nlme/html/varWeights.lmeStruct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/class.ind.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/nnet.Hess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/nnet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/predict.nnet.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/html/which.is.max.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/RngStream.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/children.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/clusterApply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/detectCores.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/makeCluster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/mcaffinity.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/mcfork.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/mclapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/mcparallel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/parallel-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/pvec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/parallel/html/splitIndices.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/car.test.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/car90.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/cu.summary.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/kyphosis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/labels.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/meanvar.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/na.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/path.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/plot.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/plotcp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/post.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/predict.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/print.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/printcp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/prune.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/residuals.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/rpart-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/rpart.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/rpart.exp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/rpart.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/rsq.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/snip.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/solder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/stagec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/summary.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/text.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/rpart/html/xpred.rpart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/Kaver.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/Kenvl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/Kfn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/Psim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/SSI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/Strauss.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/anova.trls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/correlogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/expcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/ppgetregion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/ppinit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/pplik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/ppregion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/predict.trls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/prmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/semat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/surf.gls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/surf.ls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/trls.influence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/trmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/spatial/html/variogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/asVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/backSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/bs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/interpSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/ns.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/periodicSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/polySpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/predict.bSpline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/predict.bs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/splineDesign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/splineKnots.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/splineOrder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/splines-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/splines/html/xyVector.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/AIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ARMAacf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ARMAtoMA.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Beta.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Binomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Cauchy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Chisquare.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Distributions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Exponential.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Fdist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/GammaDist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Geometric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Hypergeometric.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/IQR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/KalmanLike.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Logistic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Lognormal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Multinom.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/NLSstAsymptotic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/NLSstClosestX.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/NLSstLfAsymptote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/NLSstRtAsymptote.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/NegBinomial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Normal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Poisson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSasymp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSasympOff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSasympOrig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSbiexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSfol.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSfpl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSgompertz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSlogis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSmicmen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SSweibull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/SignRank.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/StructTS.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/TDist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Tukey.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/TukeyHSD.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Uniform.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Weibull.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/Wilcoxon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/acf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/acf2AR.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/add1.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/addmargins.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/aggregate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/alias.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/anova.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/anova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/anova.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/anova.mlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ansari.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/aov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/approxfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ar.ols.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/arima.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/arima.sim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/arima0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/as.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/asOneSidedFormula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/bandwidth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/bartlett.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/binom.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/biplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/biplot.princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/birthday.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/box.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cancor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/case.names.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/checkMFClasses.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/chisq.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cmdscale.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/complete.cases.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/confint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/constrOptim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/contrast.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/contrasts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/convolve.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cophenetic.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cor.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cov.wt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cpgram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/cutree.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/decompose.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/delete.response.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/dendrapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/density.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/deriv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/deviance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/df.residual.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/diffinv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/dist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/dummy.coef.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ecdf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/eff.aovlist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/effects.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/embed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/expand.model.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/extractAIC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/factanal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/factor.scope.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/family.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/fft.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/filter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/fisher.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/fitted.values.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/fivenum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/fligner.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/formula.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/friedman.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ftable.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ftable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/getInitial.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/glm.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/glm.summaries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/heatmap.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/identify.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/influence.measures.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/integrate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/interaction.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/is.empty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/isoreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/kernapply.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/kernel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/kmeans.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/kruskal.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ks.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ksmooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lag.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/line.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/listof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lm.influence.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lm.summaries.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lmfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/loadings.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/loess.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/logLik.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/loglin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lowess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ls.diag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ls.print.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/lsfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/mad.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/mahalanobis.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/make.link.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/makepredictcall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/manova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/mantelhaen.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/mauchly.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/mcnemar.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/median.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/medpolish.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/model.extract.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/model.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/model.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/model.tables.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/monthplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/mood.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/na.action.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/na.contiguous.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/na.fail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nafns.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/naprint.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nextn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nlm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nlminb.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nls.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/nobs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/numericDeriv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/offset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/oneway.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/optim.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/optimize.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/order.dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/p.adjust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/pairwise.prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/pairwise.t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/pairwise.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/pairwise.wilcox.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.acf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.density.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.isoreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.ppr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.profile.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.spec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.stepfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/plot.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/poisson.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/poly.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/power.anova.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/power.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/power.prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/power.t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/pp.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ppoints.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ppr.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/prcomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.HoltWinters.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.arima.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.loess.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/predict.smooth.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/preplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/print.power.htest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/print.ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/printCoefmat.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/profile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/profile.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/proj.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/prop.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/prop.trend.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/qqnorm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/quade.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/quantile.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/r2dtable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/rWishart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/read.ftable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/rect.hclust.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/relevel.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/reorder.dendrogram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/reorder.factor.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/replications.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/reshape.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/residuals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/runmed.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/scatter.smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/screeplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/sd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/se.contrast.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/selfStart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/setNames.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/shapiro.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/sigma.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/simulate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/smooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/smooth.spline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/smoothEnds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/sortedXyData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/spec.ar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/spec.pgram.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/spec.taper.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/spectrum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/splinefun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/start.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stat.anova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stats-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stats-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stats-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/step.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stepfun.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/stlmethods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/summary.aov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/summary.glm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/summary.lm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/summary.manova.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/summary.nls.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/summary.princomp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/supsmu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/symnum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/t.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/termplot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/terms.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/terms.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/terms.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/time.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/toeplitz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ts-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ts.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ts.plot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/ts.union.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/tsSmooth.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/tsdiag.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/tsp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/uniroot.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/update.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/update.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/var.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/varimax.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/vcov.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/weighted.mean.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/weighted.residuals.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/weights.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/wilcox.test.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/window.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/xtabs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats/html/zC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/coef-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/confint-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/logLik-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/mle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/plot-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/profile-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/profile.mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/show-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/stats4-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/summary-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/summary.mle-class.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/update-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/stats4/html/vcov-methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/Surv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/aeqSurv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/agreg.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/aml.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/anova.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/attrassign.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/basehaz.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/bladder.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/cch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/cgd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/cgd0.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/cipoisson.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/clogit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/cluster.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/colon.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/cox.zph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/coxph.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/coxph.detail.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/coxph.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/coxph.wtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/dsurvreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/finegray.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/flchain.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/frailty.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/genfan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/heart.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/is.ratetable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/kidney.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/lines.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/logLik.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/logan.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/lung.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/mgus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/mgus2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/model.frame.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/model.matrix.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/myeloid.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/neardate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/nwtco.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/ovarian.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/pbc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/pbcseq.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/plot.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/plot.cox.zph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/plot.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/predict.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/predict.survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/print.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/print.summary.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/print.summary.survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/print.summary.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/print.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/pspline.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/pyears.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/quantile.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/ratetable.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/ratetableDate.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/rats.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/rats2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/residuals.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/residuals.survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/retinopathy.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/rhDNase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/ridge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/stanford2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/statefig.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/strata.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/summary.aareg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/summary.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/summary.pyears.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/summary.survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/summary.survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survConcordance.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survSplit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survdiff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survexp.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survexp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survexp.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survexp.us.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survfit.coxph.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survfit.formula.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survfit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survfit.matrix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survfit.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survfitcoxph.fit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survival-internal.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survobrien.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survreg.control.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survreg.distributions.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survreg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survreg.object.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/survregDtest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/tcut.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/tmerge.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/tobin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/transplant.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/untangle.specials.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/uspop2.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/survival/html/veteran.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/TclInterface.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/TkCommands.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/TkWidgetcmds.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/TkWidgets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tclServiceMode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tcltk-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tcltk-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tkProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tkStartGUI.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tk_choose.dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tk_choose.files.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tk_messageBox.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tk_select.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tcltk/html/tkpager.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/CRANtools.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/HTMLheader.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/HTMLlinks.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/QC.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/Rcmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/Rd2HTML.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/Rd2txt_options.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/RdTextFilter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/Rdiff.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/Rdindex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/Rdutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/SweaveTeXFilter.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/add_datalist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/assertCondition.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/bibstyle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/buildVignette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/buildVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/charsets.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkFF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkMD5sums.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkPoFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkRd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkRdaFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkTnF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/checkVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/check_packages_in_dir.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/codoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/compactPDF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/delimMatch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/dependsOnPkgs.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/encoded.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/fileutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/find_gs_cmd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/getVignetteInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/loadRdMacros.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/makeLazyLoading.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/make_translations_pkg.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/makevars.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/md5sum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/package_dependencies.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/package_native_routine_registration_skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/parseLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/parse_Rd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/print.via.format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/pskill.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/psnice.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/read.00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/showNonASCII.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/startDynamicHelp.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/testInstalledPackage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/texi2dvi.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/toHTML.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/toRd.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/toTitleCase.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/tools-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/tools-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/tools-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/undoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/update_pkg_po.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/vignetteDepends.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/vignetteEngine.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/writePACKAGES.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/html/xgettext.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/00Index.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/BATCH.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/COMPILE.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/INSTALL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/LINK.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/PkgUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/Question.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/REMOVE.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/RHOME.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/RShowDoc.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/RSiteSearch.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/Rprof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/Rprofmem.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/Rscript.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/Rtangle.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/RweaveLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/SHLIB.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/Sweave.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/SweaveSyntConv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/SweaveUtils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/URLencode.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/View.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/adist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/alarm.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/apropos.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/aregexec.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/askYesNo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/aspell-utils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/aspell.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/available.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/bibentry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/browseEnv.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/browseURL.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/browseVignettes.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/bug.report.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/capture.output.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/changedFiles.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/chooseBioCmirror.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/chooseCRANmirror.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/citEntry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/citation.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/cite.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/close.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/combn.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/compareVersion.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/contrib.url.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/count.fields.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/create.post.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/data.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/dataentry.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/debugcall.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/debugger.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/demo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/download.file.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/download.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/edit.data.frame.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/example.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/file.edit.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/filetest.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/findLineNum.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/fix.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/flush.console.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/format.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/getAnywhere.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/getFromNamespace.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/getParseData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/getS3method.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/glob2rx.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/globalVariables.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/hasName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/head.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/help.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/help.request.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/help.search.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/help.start.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/hsearch-utils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/install.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/installed.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/isS3method.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/isS3stdGen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/localeToCharset.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/ls_str.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/maintainer.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/make.packages.html.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/make.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/memory.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/menu.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/methods.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/mirrorAdmin.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/modifyList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/news.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/nsl.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/object.size.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/package.skeleton.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/packageDescription.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/packageName.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/packageStatus.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/page.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/person.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/process.events.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/prompt.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/promptData.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/promptPackage.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/rcompgen.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/read.DIF.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/read.fortran.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/read.fwf.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/read.socket.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/read.table.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/recover.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/relist.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/remove.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/removeSource.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/roman.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/rtags.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/savehistory.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/select.list.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/sessionInfo.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/setRepositories.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/sourceutils.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/stack.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/str.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/strcapture.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/summaryRprof.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/tar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/toLatex.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/txtProgressBar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/type.convert.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/untar.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/unzip.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/update.packages.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/url.show.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/utils-defunct.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/utils-deprecated.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/utils-package.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/vignette.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/warnErrList.html
+ for i in '$RPM_BUILD_ROOT/usr/lib64/R/library/*/html/*.html'
+ sed -i 's|\..\/\..\/..\/doc|/usr/share/doc/R-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/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-3.5.0|g' /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/utils/html/zip.html
+ chmod +x /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/R/sh/echo.sh
+ chmod +x /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/BATCH /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/COMPILE /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/INSTALL /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/LINK /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/R /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/REMOVE /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rcmd /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rd2pdf /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rdconv /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rdiff /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rprof /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rscript /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/SHLIB /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Stangle /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Sweave /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/build /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/check /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/config /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/exec /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/f77_f2c /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/javareconf /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/libtool /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/mkinstalldirs /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/pager /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/rtags
+ chmod -x /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/mgcv/CITATION /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/R-3.5.0/CAPABILITIES
+ '[' '!' -d /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/include ']'
+ pushd /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R
~/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R ~/build/BUILD/R-3.5.0
+ ln -s ../../include/R include
+ popd
~/build/BUILD/R-3.5.0
+ '[' '!' -d /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/texmf/tex/latex/R ']'
+ mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/texmf/tex/latex
+ pushd /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/texmf/tex/latex
~/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/texmf/tex/latex ~/build/BUILD/R-3.5.0
+ ln -s ../../../R/texmf/tex/latex R
+ popd
~/build/BUILD/R-3.5.0
+ mv /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/lib/libRblas.so /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/lib/libRrefblas.so
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/R-3.5.0
extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/bin/Rscript
extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/MASS/libs/MASS.so
extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/nnet/libs/nnet.so
extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/tools/libs/tools.so
extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/library/methods/libs/methods.so
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extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/modules/lapack.so
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extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/Rscript
*** WARNING: identical binaries are copied, not linked:
        /usr/lib64/R/bin/Rscript
   and  /usr/bin/Rscript
extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/R/bin/exec/R
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extracting debug info from /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/lib64/libRmath.so
/usr/lib/rpm/sepdebugcrcfix: Updated 35 CRC32s, 0 CRC32s did match.
cpio: R-3.5.0/src/modules/lapack/SRC/iparam2stage.F: Cannot stat: No such file or directory
33402 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.aL0xlh
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.5.0
+ exit 0
Processing files: R-3.5.0-1.el7.ppc64
Provides: R = 3.5.0-1.el7 R(ppc-64) = 3.5.0-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Processing files: R-core-3.5.0-1.el7.ppc64
Provides: R-KernSmooth = 2.23.15 R-MASS = 7.3.49 R-Matrix = 1.2.14 R-base = 3.5.0 R-boot = 1.3.20 R-class = 7.3.14 R-cluster = 2.0.7.1 R-codetools = 0.2.15 R-core = 3.5.0-1.el7 R-core(ppc-64) = 3.5.0-1.el7 R-datasets = 3.5.0 R-foreign = 0.8.70 R-grDevices = 3.5.0 R-graphics = 3.5.0 R-grid = 3.5.0 R-lattice = 0.20.35 R-methods = 3.5.0 R-mgcv = 1.8.23 R-nlme = 3.1.137 R-nnet = 7.3.12 R-parallel = 3.5.0 R-rpart = 4.1.13 R-spatial = 7.3.11 R-splines = 3.5.0 R-stats = 3.5.0 R-stats4 = 3.5.0 R-survival = 2.41.3 R-tcltk = 3.5.0 R-tools = 3.5.0 R-utils = 3.5.0 config(R-core) = 3.5.0-1.el7 libR.so()(64bit) libRlapack.so()(64bit) libRrefblas.so()(64bit)
Requires(interp): /bin/sh /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(preun): /bin/sh
Requires(postun): /bin/sh
Requires(posttrans): /bin/sh
Requires: /bin/bash /bin/sh ld64.so.1()(64bit) ld64.so.1(GLIBC_2.3)(64bit) libICE.so.6()(64bit) libR.so()(64bit) libRblas.so()(64bit) libRlapack.so()(64bit) libSM.so.6()(64bit) libX11.so.6()(64bit) libXext.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_2.15)(64bit) libc.so.6(GLIBC_2.16)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(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) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.3)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgfortran.so.3()(64bit) libgfortran.so.3(GFORTRAN_1.0)(64bit) libglib-2.0.so.0()(64bit) libgobject-2.0.so.0()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libicui18n.so.50()(64bit) libicuuc.so.50()(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_2.3)(64bit) libm.so.6(GLIBC_2.4)(64bit) libpango-1.0.so.0()(64bit) libpangocairo-1.0.so.0()(64bit) libpcre.so.1()(64bit) libpng15.so.15()(64bit) libpng15.so.15(PNG15_0)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.3)(64bit) libreadline.so.6()(64bit) librt.so.1()(64bit) librt.so.1(GLIBC_2.3)(64bit) libtcl8.5.so()(64bit) libtiff.so.5()(64bit) libtiff.so.5(LIBTIFF_4.0)(64bit) libtk8.5.so()(64bit) libtre.so.5()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Obsoletes: R-Matrix < 0.999375-7
Processing files: R-core-devel-3.5.0-1.el7.ppc64
Provides: R-Matrix-devel = 1.2.14 R-core-devel = 3.5.0-1.el7 R-core-devel(ppc-64) = 3.5.0-1.el7 pkgconfig(libR) = 3.5.0
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-3.5.0-1.el7.ppc64
Provides: R-devel = 3.5.0-1.el7 R-devel(ppc-64) = 3.5.0-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Processing files: R-java-3.5.0-1.el7.ppc64
Provides: R-java = 3.5.0-1.el7 R-java(ppc-64) = 3.5.0-1.el7
Requires(interp): /bin/sh
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Requires(post): R-core = 3.5.0-1.el7 /bin/sh
Processing files: R-java-devel-3.5.0-1.el7.ppc64
Provides: R-java-devel = 3.5.0-1.el7 R-java-devel(ppc-64) = 3.5.0-1.el7
Requires(interp): /bin/sh
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Requires(post): R-core-devel = 3.5.0-1.el7 java-devel /bin/sh
Processing files: libRmath-3.5.0-1.el7.ppc64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.f2ryUi
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.5.0
+ DOCDIR=/builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/libRmath-3.5.0
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/libRmath-3.5.0
+ cp -pr doc/COPYING /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64/usr/share/doc/libRmath-3.5.0
+ exit 0
Provides: libRmath = 3.5.0-1.el7 libRmath(ppc-64) = 3.5.0-1.el7 libRmath.so()(64bit)
Requires(interp): /sbin/ldconfig /sbin/ldconfig
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /sbin/ldconfig
Requires(postun): /sbin/ldconfig
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgomp.so.1()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.3)(64bit) libm.so.6(GLIBC_2.4)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.3)(64bit) rtld(GNU_HASH)
Processing files: libRmath-devel-3.5.0-1.el7.ppc64
Provides: libRmath-devel = 3.5.0-1.el7 libRmath-devel(ppc-64) = 3.5.0-1.el7 pkgconfig(libRmath) = 3.5.0
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-3.5.0-1.el7.ppc64
Provides: libRmath-static = 3.5.0-1.el7 libRmath-static(ppc-64) = 3.5.0-1.el7
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-debuginfo-3.5.0-1.el7.ppc64
Provides: R-debuginfo = 3.5.0-1.el7 R-debuginfo(ppc-64) = 3.5.0-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64
Wrote: /builddir/build/RPMS/R-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/R-core-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/R-core-devel-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/R-devel-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/R-java-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/R-java-devel-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/libRmath-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/libRmath-devel-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/libRmath-static-3.5.0-1.el7.ppc64.rpm
Wrote: /builddir/build/RPMS/R-debuginfo-3.5.0-1.el7.ppc64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ALkrkQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd R-3.5.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-3.5.0-1.el7.ppc64
+ exit 0
Child return code was: 0