Mock Version: 1.1.32
Mock Version: 1.1.32
ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target i686 --nodeps builddir/build/SPECS/coot.spec'], False, '/var/lib/mock/f19-build-1812387-313193/root/', None, 86400, True, False, 500, 425, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}, logger=<mockbuild.trace_decorator.getLog object at 0x12f8310>)
Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target i686 --nodeps builddir/build/SPECS/coot.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}
sh: /usr/bin/python: No such file or directory
sh: /usr/bin/python: No such file or directory
sh: /usr/bin/python: No such file or directory
sh: /usr/bin/python: No such file or directory
sh: /usr/bin/python: No such file or directory
sh: /usr/bin/python: No such file or directory
sh: /usr/bin/python: No such file or directory
warning: Could not canonicalize hostname: buildvm-04.phx2.fedoraproject.org
Building target platforms: i686
Building for target i686
Wrote: /builddir/build/SRPMS/coot-0.7-5.20120929svn4458.fc19.src.rpm
Child return code was: 0
LEAVE do --> 

ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/coot.spec'], False, '/var/lib/mock/f19-build-1812387-313193/root/', None, 86400, True, False, 500, 425, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}, logger=<mockbuild.trace_decorator.getLog object at 0x12f8310>)
Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/coot.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}
Building target platforms: i686
Building for target i686
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.RlPKXI
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf coot-0.7
+ /usr/bin/xz -dc /builddir/build/SOURCES/coot-0.7-20120929svn4458.tar.xz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd coot-0.7
+ /usr/bin/gzip -dc /builddir/build/SOURCES/coot-reference-structures.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (coot-configure.in.patch):
+ echo 'Patch #0 (coot-configure.in.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/coot-configure.in.patch
+ /usr/bin/patch -p0 --fuzz=0
patching file configure.in
Patch #1 (coot-user-manual.texi.patch):
+ echo 'Patch #1 (coot-user-manual.texi.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/coot-user-manual.texi.patch
+ /usr/bin/patch -p0 --fuzz=0
patching file doc/coot-user-manual.texi
Patch #2 (coot-unistd.patch):
+ echo 'Patch #2 (coot-unistd.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/coot-unistd.patch
+ /usr/bin/patch -p0 --fuzz=0
patching file utils/coot-utils.cc
Patch #3 (coot-makefile.patch):
+ echo 'Patch #3 (coot-makefile.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/coot-makefile.patch
+ /usr/bin/patch -p0 --fuzz=0
patching file lbg/Makefile.am
Patch #4 (coot-ssm1.3.patch):
+ echo 'Patch #4 (coot-ssm1.3.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/coot-ssm1.3.patch
+ /usr/bin/patch -p0 --fuzz=0
(Stripping trailing CRs from patch; use --binary to disable.)
patching file ./src/graphics-info.h
Hunk #1 succeeded at 3305 (offset -2 lines).
Hunk #2 succeeded at 3313 (offset -2 lines).
Hunk #3 succeeded at 3323 (offset -2 lines).
(Stripping trailing CRs from patch; use --binary to disable.)
patching file ./src/graphics-info-superpose.cc
(Stripping trailing CRs from patch; use --binary to disable.)
patching file ./src/molecule-class-info-ncs.cc
Patch #5 (coot-guile.patch):
+ echo 'Patch #5 (coot-guile.patch):'
+ /usr/bin/cat /builddir/build/SOURCES/coot-guile.patch
+ /usr/bin/patch -p0 --fuzz=0
patching file macros/guile.m4
+ cp /builddir/build/SOURCES/svn-revision.cc ./src/
+ cp /builddir/build/SOURCES/coot.in ./src/
+ rm src/coot_wrap_guile_pre.cc
+ rm src/coot_wrap_python_pre.cc
+ iconv -f iso8859-1 -t utf-8 README
+ mv -f README.conv README
+ aclocal -I macros
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
+ libtoolize --automake --copy
+ autoconf
+ automake --copy --add-missing --gnu
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
configure.in:31: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated.  For more info, see:
configure.in:31: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
analysis/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
angles/Makefile.am:9: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/catcheck/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/rama/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/sec-str/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/strand-analysis/Makefile.am:5: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/vectors/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
build/Makefile.am:25: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
ccp4mg-utils/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
coords/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
coot-surface/Makefile.am:21: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
coot-utils/Makefile.am:36: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
cootaneer/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
cootilus/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
db-main/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
density-contour/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
geometry/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
goograph/Makefile.am:22: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
high-res/Makefile.am:29: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
ideal/Makefile.am:32: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
lbg/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
libgtkgraph/Makefile.am:2: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
lidia-core/Makefile.am:26: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
ligand/Makefile.am:26: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
mini-mol/Makefile.am:25: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
protein_db/Makefile.am:22: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
skeleton/Makefile.am:24: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/Makefile.am:186: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
surface/Makefile.am:2: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
tw/Makefile.am:28: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
utils/Makefile.am:21: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.AS5cYp
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.7
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro '
+ export LDFLAGS
++ find . -name config.guess -o -name config.sub
+ for i in '$(find . -name config.guess -o -name config.sub)'
++ basename ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
++ basename ./config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
+ for i in '$(find . -name config.guess -o -name config.sub)'
++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ ./configure --build=i686-redhat-linux-gnu --host=i686-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/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-gtk2 --with-guile --with-python --with-pygtk --with-gtkcanvas-prefix=/usr --disable-static 'CPPFLAGS=-I/usr/include/mmdb -I/usr/include/ssm' 'CXXFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing'
configure: WARNING: unrecognized options: --with-gtkcanvas-prefix
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/builddir/build/BUILD/coot-0.7/missing: Unknown `--is-lightweight' option
Try `/builddir/build/BUILD/coot-0.7/missing --help' for more information
checking for a thread-safe mkdir -p... configure: WARNING: 'missing' script is too old or missing
/usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for i686-redhat-linux-gnu-gcc... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... none
checking for library containing strerror... none required
checking for i686-redhat-linux-gnu-gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) none
checking for i686-redhat-linux-gnu-gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for i686-redhat-linux-gnu-g++... no
checking for i686-redhat-linux-gnu-c++... no
checking for i686-redhat-linux-gnu-gpp... no
checking for i686-redhat-linux-gnu-aCC... no
checking for i686-redhat-linux-gnu-CC... no
checking for i686-redhat-linux-gnu-cxx... no
checking for i686-redhat-linux-gnu-cc++... no
checking for i686-redhat-linux-gnu-cl.exe... no
checking for i686-redhat-linux-gnu-FCC... no
checking for i686-redhat-linux-gnu-KCC... no
checking for i686-redhat-linux-gnu-RCC... no
checking for i686-redhat-linux-gnu-xlC_r... no
checking for i686-redhat-linux-gnu-xlC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking build system type... i686-redhat-linux-gnu
checking host system type... i686-redhat-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1966080
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert i686-redhat-linux-gnu file names to i686-redhat-linux-gnu format... func_convert_file_noop
checking how to convert i686-redhat-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for i686-redhat-linux-gnu-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for i686-redhat-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for i686-redhat-linux-gnu-ar... no
checking for ar... ar
checking for archiver @FILE support... @
checking for i686-redhat-linux-gnu-strip... no
checking for strip... strip
checking for i686-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for i686-redhat-linux-gnu-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking for gcc option to support OpenMP... -fopenmp
checking for i686-redhat-linux-gnu-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GLIB... yes
checking if this is MINGW on Windows... no
checking for MMDB... yes
checking for MMDBSSM... yes
checking for CLIPPER... yes
Congratulations, you are using Guile
checking for guile1.8... /usr/bin/guile1.8
checking for guile1.8-config... /usr/bin/guile1.8-config
checking for guile1.8-tools... /usr/bin/guile1.8-tools
checking libguile compile flags...   -pthread
checking libguile link flags...  -pthread  -lguile 
checking for Guile-Lib... yes
checking GUILE_VERSION: 1.8
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.3... yes
checking for GTK... yes
checking for GNOME_CANVAS... yes
checking for pkg-config... /usr/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0)
checking for glLineWidth in -lGL... yes
checking for GLUT... yes
checking for Python... checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
Cool, using Python
checking for PYGTK... yes
Good we have pygtk
checking for guile-gtk... 
checking libglade... no
checking for Goocanvas... yes
Not using database
checking for curl >= 7.9.7... ./configure: line 19353: bc: command not found
7.29.0
checking build type... Linux-i386-fedora-19-python-gtk2
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating macros/Makefile
config.status: creating pdb-templates/Makefile
config.status: creating scheme/Makefile
config.status: creating python/Makefile
config.status: creating compat/Makefile
config.status: creating utils/Makefile
config.status: creating coot-utils/Makefile
config.status: creating protein_db/Makefile
config.status: creating ccp4mg-utils/Makefile
config.status: creating coords/Makefile
config.status: creating db-main/Makefile
config.status: creating density-contour/Makefile
config.status: creating surface/Makefile
config.status: creating coot-surface/Makefile
config.status: creating angles/Makefile
config.status: creating mini-mol/Makefile
config.status: creating skeleton/Makefile
config.status: creating ligand/Makefile
config.status: creating geometry/Makefile
config.status: creating ideal/Makefile
config.status: creating build/Makefile
config.status: creating analysis/Makefile
config.status: creating high-res/Makefile
config.status: creating tw/Makefile
config.status: creating cootaneer/Makefile
config.status: creating cootilus/Makefile
config.status: creating greg-tests/Makefile
config.status: creating python-tests/Makefile
config.status: creating lidia-core/Makefile
config.status: creating libgtkgraph/Makefile
config.status: creating goograph/Makefile
config.status: creating lbg/Makefile
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/coot
config.status: creating python/coot_load_modules.py
config.status: creating data/Makefile
config.status: creating rama-data/Makefile
config.status: creating auxil/Makefile
config.status: creating auxil/catcheck/Makefile
config.status: creating auxil/rama/Makefile
config.status: creating auxil/sec-str/Makefile
config.status: creating auxil/strand-analysis/Makefile
config.status: creating auxil/vectors/Makefile
config.status: creating rcrane/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --with-gtkcanvas-prefix
+ sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
+ sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
+ make -j5
Making all in auxil
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
Making all in catcheck
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
Making all in rama
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
Making all in sec-str
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
Making all in strand-analysis
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
Making all in vectors
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
Making all in scheme
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/scheme'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/scheme'
Making all in python
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/python'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/python'
Making all in pdb-templates
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
Making all in macros
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/macros'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/macros'
Making all in compat
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/compat'
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o getopt.lo getopt.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o getopt1.lo getopt1.c
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c getopt1.c  -fPIC -DPIC -o .libs/getopt1.o
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables  -Wl,-z,relro  -o libcoot-compat.la -rpath /usr/lib getopt.lo getopt1.lo  
libtool: link: gcc -shared  -fPIC -DPIC  .libs/getopt.o .libs/getopt1.o    -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-compat.so.0 -o .libs/libcoot-compat.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-compat.so.0" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-compat.so" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/compat'
Making all in utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/utils'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		  -I/usr/include/mmdb -I/usr/include/ssm  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-utils.lo coot-utils.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		  -I/usr/include/mmdb -I/usr/include/ssm  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-fasta.lo coot-fasta.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		  -I/usr/include/mmdb -I/usr/include/ssm  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o atomic-numbers.lo atomic-numbers.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		  -I/usr/include/mmdb -I/usr/include/ssm  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o gdk-keysyms.lo gdk-keysyms.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		  -I/usr/include/mmdb -I/usr/include/ssm  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o hsv-rgb.lo hsv-rgb.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-fasta.cc  -fPIC -DPIC -o .libs/coot-fasta.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-utils.cc  -fPIC -DPIC -o .libs/coot-utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c hsv-rgb.cc  -fPIC -DPIC -o .libs/hsv-rgb.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c gdk-keysyms.cc  -fPIC -DPIC -o .libs/gdk-keysyms.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c atomic-numbers.cc  -fPIC -DPIC -o .libs/atomic-numbers.o
coot-utils.cc: In function 'std::string coot::util::remove_trailing_whitespace(const string&)':
coot-utils.cc:298:8: warning: unused variable 'cutpoint' [-Wunused-variable]
    int cutpoint = 0;
        ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-utils.la -rpath /usr/lib coot-utils.lo coot-fasta.lo atomic-numbers.lo gdk-keysyms.lo hsv-rgb.lo  
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-utils.o .libs/coot-fasta.o .libs/atomic-numbers.o .libs/gdk-keysyms.o .libs/hsv-rgb.o   -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-utils.so.0 -o .libs/libcoot-utils.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-utils.so.0" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-utils.so" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/utils'
Making all in protein_db
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/protein_db'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o protein_db.lo protein_db.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o protein_db_utils.lo protein_db_utils.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rna_db.lo rna_db.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c protein_db.cpp  -fPIC -DPIC -o .libs/protein_db.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c protein_db_utils.cpp  -fPIC -DPIC -o .libs/protein_db_utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c rna_db.cpp  -fPIC -DPIC -o .libs/rna_db.o
protein_db_utils.cpp: In constructor 'ProteinDB::ScoreClashes::ScoreClashes(const std::vector<clipper::Coord_orth>&, const clipper::Spacegroup&, const clipper::Cell&, double)':
protein_db_utils.cpp:91:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < coords.size(); i++ ) {
                                    ^
protein_db_utils.cpp: In member function 'void ProteinDB::ScoreClashes::set_exclude(const std::vector<clipper::Coord_orth>&, double)':
protein_db_utils.cpp:126:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int a = 0; a < coords.size(); a++ ) {
                                    ^
protein_db_utils.cpp:128:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < atoms.size(); i++ )
                                     ^
protein_db_utils.cpp: In member function 'double ProteinDB::ScoreClashes::score(const ProteinDB::Chain&) const':
protein_db_utils.cpp:176:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < atoms.size(); i++ )
                                     ^
protein_db_utils.cpp: In member function 'std::vector<ProteinDB::Chain> ProteinDB::ProteinDBSearch::search(const ProteinDB::Chain&, int, ProteinDB::ScoreDensity&, ProteinDB::ScoreClashes&, double, double)':
protein_db_utils.cpp:213:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f = 0; f < frags.size(); f++ ) {
                                     ^
protein_db_utils.cpp:228:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f = 0; f < frags.size(); f++ ) {
                                     ^
protein_db.cpp: In member function 'bool ProteinDB::Chain::save_db(clipper::String) const':
protein_db.cpp:244:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < dbresidues.size(); r++ ) {
                                        ^
protein_db.cpp: In member function 'bool ProteinDB::Chain::load_db(clipper::String)':
protein_db.cpp:272:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < dbresidues.size(); r++ ) {
                                        ^
protein_db.cpp: In member function 'bool ProteinDB::Chain::merge(const ProteinDB::Chain&, const std::vector<double>&)':
protein_db.cpp:282:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( wgt.size() != 3*size() ) return false;
                             ^
protein_db.cpp:283:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < dbresidues.size(); r++ )
                                        ^
protein_db.cpp: In member function 'bool ProteinDB::Chain::is_continuous() const':
protein_db.cpp:303:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbresidues.size()-1; i++ ) {
                                          ^
protein_db.cpp: In member function 'void ProteinDB::Chain::transform(const clipper::RTop_orth&)':
protein_db.cpp:318:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < dbresidues.size(); r++ )
                                        ^
protein_db.cpp: In member function 'double ProteinDB::Chain::rmsd(const ProteinDB::Chain&) const':
protein_db.cpp:354:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbresidues.size(); i++ ) {
                                        ^
protein_db.cpp: In member function 'double ProteinDB::Chain::rmsd(const ProteinDB::Chain&, const std::vector<double>&) const':
protein_db.cpp:368:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbresidues.size(); i++ ) {
                                        ^
protein_db.cpp: In member function 'void ProteinDB::Chain::debug() const':
protein_db.cpp:382:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < dbresidues.size(); r++ ) {
                                        ^
protein_db.cpp: In member function 'void ProteinDB::ChainDB::calc_distances()':
protein_db.cpp:412:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbresidues.size()-1; i++ ) {
                                          ^
protein_db.cpp:425:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbdistvecs.size(); i++ ) {
                                        ^
protein_db.cpp: In member function 'double ProteinDB::ChainDB::score_distance(const ProteinDB::ChainDB&, int, double, const std::vector<ProteinDB::Residue::TypeMask>&) const':
protein_db.cpp:547:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < types.size(); i++ )
                                   ^
protein_db.cpp: In member function 'std::vector<int> ProteinDB::ChainDB::match_fragment_preliminary(const ProteinDB::ChainDB&, int) const':
protein_db.cpp:566:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbresidues.size(); i++ ) {
                                        ^
protein_db.cpp:570:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( scores_dist.size() >= 2*nhit ) {  // optimisation
                                  ^
protein_db.cpp:582:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( i < scores_dist.size() )
                               ^
protein_db.cpp: In member function 'std::vector<ProteinDB::Chain> ProteinDB::ChainDB::match_fragment(const ProteinDB::ChainDB&, int, int) const':
protein_db.cpp:610:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < scores_dist.size(); i++ ) {
                                         ^
protein_db.cpp:618:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( scores_lsq.size() > nlsq ) scores_lsq.resize( nlsq );
                            ^
protein_db.cpp:622:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < scores_lsq.size(); i++ ) {
                                        ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-protein-db.la -rpath /usr/lib protein_db.lo protein_db_utils.lo rna_db.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/protein_db.o .libs/protein_db_utils.o .libs/rna_db.o   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-protein-db.so.0 -o .libs/libcoot-protein-db.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-protein-db.so.0" && ln -s "libcoot-protein-db.so.0.0.0" "libcoot-protein-db.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-protein-db.so" && ln -s "libcoot-protein-db.so.0.0.0" "libcoot-protein-db.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-protein-db.la" && ln -s "../libcoot-protein-db.la" "libcoot-protein-db.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/protein_db'
Making all in mini-mol
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/mini-mol'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o mini-mol.lo mini-mol.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o mini-mol-utils.lo mini-mol-utils.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o atom-quads.lo atom-quads.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o testminimol.o testminimol.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mini-mol.cc  -fPIC -DPIC -o .libs/mini-mol.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c atom-quads.cc  -fPIC -DPIC -o .libs/atom-quads.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mini-mol-utils.cc  -fPIC -DPIC -o .libs/mini-mol-utils.o
testminimol.cc: In function 'int main(int, char**)':
testminimol.cc:53:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int ifrag=0; ifrag<m2.fragments.size(); ifrag++)
                                                ^
atom-quads.cc: In member function 'coot::atom_quad coot::atom_quad::setup_chiral_quad(CResidue*, CResidue*, const string&, const std::vector<std::basic_string<char> >&) const':
atom-quads.cc:141:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
atom-quads.cc:154:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
atom-quads.cc: In member function 'double coot::atom_index_quad::torsion(CResidue*) const':
atom-quads.cc:206:11: warning: unused variable 'angle' [-Wunused-variable]
    double angle = 0;
           ^
atom-quads.cc: In member function 'double coot::atom_index_quad::torsion(PPCAtom, int) const':
atom-quads.cc:221:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_selected_atoms; i++) {
                             ^
mini-mol-utils.cc: In function 'std::pair<bool, clipper::Coord_orth> coot::cbeta_position(const coot::minimol::residue&)':
mini-mol-utils.cc:44:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iat=0; iat<res.atoms.size(); iat++) {
                                       ^
mini-mol-utils.cc: In function 'std::pair<bool, clipper::Coord_orth> coot::o_position(const coot::minimol::residue&, const coot::minimol::residue&)':
mini-mol-utils.cc:133:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iat=0; iat<res_with_N.atoms.size(); iat++) {
                                              ^
mini-mol-utils.cc:141:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iat=0; iat<res_with_CA_C.atoms.size(); iat++) {
                                                 ^
mini-mol.cc: In constructor 'coot::minimol::molecule::molecule(PPCAtom, int, const std::vector<CAtom>&)':
mini-mol.cc:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (atoms.size() != n_residues_atoms) {
                        ^
mini-mol.cc: In member function 'void coot::minimol::residue::delete_atom_indices(const std::vector<int>&)':
mini-mol.cc:680:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (iat == atom_indices[iind]) {
                               ^
mini-mol.cc: In member function 'std::vector<coot::minimol::atom*> coot::minimol::residue::select_atoms_serial() const':
mini-mol.cc:738:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iatom=0; iatom<natoms; iatom++) {
                                     ^
mini-mol.cc: In member function 'coot::minimol::molecule coot::minimol::molecule::molecule_of_atom_types(std::string) const':
mini-mol.cc:948:99: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int ires=fragments[ifr].min_res_no(); ires<=fragments[ifr].max_residue_number(); ires++)
                                                                                                   ^
mini-mol.cc: In member function 'int coot::minimol::molecule::set_atom_occ(const string&, float)':
mini-mol.cc:1239:99: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int ires=fragments[ifr].min_res_no(); ires<=fragments[ifr].max_residue_number(); ires++)
                                                                                                   ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-mini-mol.la -rpath /usr/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb    
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so.0" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o testminimol testminimol.o libcoot-mini-mol.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/testminimol testminimol.o  ./.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/mini-mol'
Making all in geometry
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/geometry'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o protein-geometry.lo protein-geometry.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o protein-geometry-mmdb.lo protein-geometry-mmdb.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o read-sbase.lo read-sbase.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o energy-lib.lo energy-lib.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o chem_mods.lo chem_mods.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c protein-geometry-mmdb.cc  -fPIC -DPIC -o .libs/protein-geometry-mmdb.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c energy-lib.cc  -fPIC -DPIC -o .libs/energy-lib.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c chem_mods.cc  -fPIC -DPIC -o .libs/chem_mods.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c read-sbase.cc  -fPIC -DPIC -o .libs/read-sbase.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c protein-geometry.cc  -fPIC -DPIC -o .libs/protein-geometry.o
energy-lib.cc: In member function 'void coot::energy_lib_t::read(const string&)':
energy-lib.cc:79:9: warning: unused variable 'n_chiral' [-Wunused-variable]
     int n_chiral = 0;
         ^
energy-lib.cc: In member function 'void coot::energy_lib_t::add_energy_lib_angles(PCMMCIFLoop)':
energy-lib.cc:290:16: warning: unused variable 'spring_const' [-Wunused-variable]
       realtype spring_const;
                ^
energy-lib.cc: In member function 'coot::energy_lib_bond coot::energy_lib_t::get_bond(const string&, const string&, const string&, bool) const':
energy-lib.cc:564:12: warning: variable 'permissive_bond_order' set but not used [-Wunused-but-set-variable]
       bool permissive_bond_order = false;
            ^
read-sbase.cc: In member function 'void coot::protein_geometry::read_sbase_residues()':
read-sbase.cc:41:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<local_residue_codes.size(); i++) {
                                                ^
protein-geometry.cc: In member function 'void coot::protein_geometry::mon_lib_add_tree(std::string, std::string, std::string, std::string, std::string)':
protein-geometry.cc:901:9: warning: variable 'ifound' set but not used [-Wunused-but-set-variable]
    bool ifound = 0;
         ^
chem_mods.cc: In member function 'int coot::protein_geometry::add_mod(PCMMCIFData)':
chem_mods.cc:161:7: warning: unused variable 'n_chiral' [-Wunused-variable]
   int n_chiral = 0;
       ^
chem_mods.cc:151:8: warning: unused variable 'r' [-Wunused-variable]
    int r = 0; 
        ^
chem_mods.cc: In member function 'std::pair<coot::protein_geometry::chem_mod, coot::protein_geometry::chem_mod> coot::protein_geometry::get_chem_mods_for_link(const string&) const':
chem_mods.cc:611:9: warning: unused variable 'found' [-Wunused-variable]
    bool found = false; 
         ^
protein-geometry.cc: In function 'std::ostream& coot::operator<<(std::ostream&, coot::dict_plane_restraint_t)':
protein-geometry.cc:1446:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iatom=0; iatom<rest.n_atoms(); iatom++) {
                                                  ^
protein-geometry.cc: In member function 'int coot::protein_geometry::comp_atom(PCMMCIFLoop)':
protein-geometry.cc:1706:11: warning: unused variable 'ierr_optional' [-Wunused-variable]
       int ierr_optional;
           ^
protein-geometry.cc: In member function 'int coot::protein_geometry::add_chem_mods(PCMMCIFData)':
protein-geometry.cc:2428:7: warning: unused variable 'n_chiral' [-Wunused-variable]
   int n_chiral = 0;
       ^
protein-geometry.cc: In member function 'void coot::protein_geometry::add_synonyms(PCMMCIFData)':
protein-geometry.cc:2450:7: warning: unused variable 'n_chiral' [-Wunused-variable]
   int n_chiral = 0;
       ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-graph.lo lbg-graph.cc
protein-geometry.cc: In member function 'std::vector<coot::dict_chiral_restraint_t> coot::protein_geometry::get_monomer_chiral_volumes(std::string) const':
protein-geometry.cc:4207:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<dict_res_restraints.size(); i++) {
                                                ^
protein-geometry.cc: In member function 'std::pair<bool, std::vector<std::basic_string<char> > > coot::protein_geometry::atoms_match_dictionary(CResidue*, bool, bool, const coot::dictionary_residue_restraints_t&) const':
protein-geometry.cc:4432:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_residue_atoms; i++) {
                             ^
protein-geometry.cc: In member function 'bool coot::protein_geometry::atoms_match_dictionary_bond_distance_check(CResidue*, bool, const coot::dictionary_residue_restraints_t&) const':
protein-geometry.cc:4530:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<(n_residue_atoms-1); iat++) {
                                                  ^
protein-geometry.cc:4534:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int jat=iat+1; jat<n_residue_atoms; jat++) {
                                          ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lbg-graph.cc  -fPIC -DPIC -o .libs/lbg-graph.o
protein-geometry.cc: In member function 'void coot::protein_geometry::remove_omega_peptide_restraints()':
protein-geometry.cc:5158:9: warning: variable 'ifound' set but not used [-Wunused-but-set-variable]
    bool ifound = 0;
         ^
protein-geometry.cc: In member function 'bool coot::dictionary_residue_restraints_t::is_redundant_plane_resetraints(std::vector<coot::dict_plane_restraint_t>::iterator)':
protein-geometry.cc:5241:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int j=0; j<it_this->n_atoms(); j++) {
                                                ^
protein-geometry.cc:5242:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i=0; i<it_ref->n_atoms(); i++) {
                                                  ^
protein-geometry.cc: In member function 'void coot::dictionary_residue_restraints_t::write_cif(const string&) const':
protein-geometry.cc:5324:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<atom_info.size(); i++) {
                                      ^
protein-geometry.cc:5328:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (n_atoms_with_coords == atom_info.size())
                                                 ^
protein-geometry.cc:5334:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<atom_info.size(); i++) {
                                     ^
protein-geometry.cc:5365:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<bond_restraint.size(); i++) {
                                          ^
protein-geometry.cc:5396:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<angle_restraint.size(); i++) {
                                           ^
protein-geometry.cc:5424:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<torsion_restraint.size(); i++) {
                                             ^
protein-geometry.cc:5454:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<chiral_restraint.size(); i++) {
                                            ^
protein-geometry.cc:5485:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<plane_restraint.size(); i++) {
                                           ^
protein-geometry.cc:5266:9: warning: unused variable 'S' [-Wunused-variable]
    char S[2000];
         ^
protein-geometry.cc: In member function 'std::vector<std::basic_string<char> > coot::protein_geometry::monomer_types() const':
protein-geometry.cc:5832:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<dict_res_restraints.size(); i++) {
                                             ^
protein-geometry.cc: In member function 'std::string coot::protein_geometry::get_group(const string&) const':
protein-geometry.cc:5864:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<size(); i++) {
                                  ^
protein-geometry.cc: In member function 'CResidue* coot::protein_geometry::get_residue(const string&, bool)':
protein-geometry.cc:5900:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<dict_res_restraints.size(); i++) {
                                             ^
protein-geometry.cc:5895:9: warning: unused variable 'r' [-Wunused-variable]
    bool r = have_dictionary_for_residue_type(comp_id, 42);
         ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-geometry.o test-geometry.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../mini-mol -I../coot-utils -I../compat  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-read-components.o test-read-components.cc
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo chem_mods.lo lbg-graph.lo ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/lbg-graph.o   ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so.0" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-geometry test-geometry.o ./libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-read-components test-read-components.o ./libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-geometry test-geometry.o  ./.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
libtool: link: g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-read-components test-read-components.o  ./.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/geometry'
Making all in coot-utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-utils'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-coord-utils.lo coot-coord-utils.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-coord-utils-nucleotides.lo coot-coord-utils-nucleotides.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-rama.lo coot-rama.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-h-bonds.lo coot-h-bonds.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o hole.lo hole.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-h-bonds.cc  -fPIC -DPIC -o .libs/coot-h-bonds.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-rama.cc  -fPIC -DPIC -o .libs/coot-rama.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c hole.cc  -fPIC -DPIC -o .libs/hole.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-coord-utils.cc  -fPIC -DPIC -o .libs/coot-coord-utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-coord-utils-nucleotides.cc  -fPIC -DPIC -o .libs/coot-coord-utils-nucleotides.o
In file included from coot-rama.cc:29:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from hole.cc:5:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-coord-utils.cc:30:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-coord-utils.cc: In function 'std::vector<CResidue*> coot::filter_residues_by_solvent_contact(CResidue*, CMMDBManager*, const std::vector<CResidue*>&, const double&)':
coot-coord-utils.cc:497:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int jat=0; jat<n_lig_residue_atoms; jat++) {
                                ^
coot-coord-utils.cc:502:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                   ^
coot-coord-utils.cc: In function 'std::pair<bool, clipper::Coord_orth> coot::util::get_residue_centre(CResidue*)':
coot-coord-utils.cc:1178:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++) {
                                ^
In file included from coot-coord-utils-nucleotides.cc:26:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-coord-utils.cc: In member function 'void coot::graph_match_info_t::match_names(CResidue*)':
coot-coord-utils.cc:1966:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
coot-coord-utils.cc:2024:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
coot-coord-utils-nucleotides.cc: In member function 'void coot::pucker_analysis_info_t::assign_base_atom_coords(CResidue*)':
coot-coord-utils-nucleotides.cc:189:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_residue_atoms; i++) { 
                             ^
coot-coord-utils.cc: In function 'void coot::util::delete_alt_confs_except(CResidue*, const string&)':
coot-coord-utils.cc:2239:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_residue_atoms; i++) { 
                             ^
coot-coord-utils.cc: In function 'CAtom* coot::util::get_atom(const coot::atom_spec_t&, CMMDBManager*)':
coot-coord-utils.cc:2423:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                    ^
coot-coord-utils.cc: In function 'std::pair<CMMDBManager*, int> coot::util::create_mmdbmanager_from_res_selection(CMMDBManager*, CResidue**, int, int, int, const string&, const string&, short int)':
coot-coord-utils.cc:2637:13: warning: variable 'residue_p' set but not used [-Wunused-but-set-variable]
   PCResidue residue_p;
             ^
coot-coord-utils.cc: In function 'void coot::util::transform_selection(CMMDBManager*, int, const clipper::RTop_orth&)':
coot-coord-utils.cc:3269:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_selected_atoms; iat++) {
                                 ^
In file included from coot-h-bonds.hh:12:0,
                 from coot-h-bonds.cc:22:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-coord-utils.cc: In function 'std::map<std::basic_string<char>, clipper::RTop_orth> coot::util::get_ori_to_this_res(CResidue*)':
coot-coord-utils.cc:3614:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                 ^
coot-coord-utils.cc:3618:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                 ^
hole.cc: In member function 'std::pair<std::vector<std::pair<clipper::Coord_orth, double> >, std::vector<coot::hole_surface_point_t> > coot::hole::generate()':
hole.cc:146:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int istep=0; istep<=nsteps; istep++) {
                                      ^
hole.cc: In member function 'double coot::hole::sphere_size(const clipper::Coord_orth&, int) const':
hole.cc:276:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_selected_atoms; iat++) {
                                 ^
hole.cc:264:11: warning: unused variable 'r' [-Wunused-variable]
    double r = -1;
           ^
hole.cc: In member function 'std::vector<coot::hole_surface_point_t> coot::hole::get_surface_points(const std::vector<std::pair<clipper::Coord_orth, double> >&) const':
hole.cc:417:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (max_downstream_check_limit>=probe_path.size())
                                                       ^
hole.cc:449:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int iprev=max_upstream_check_limit; iprev<=max_downstream_check_limit; iprev++) {
                                                                  ^
hole.cc:401:11: warning: unused variable 'dot_density' [-Wunused-variable]
    double dot_density = 0.35;
           ^
coot-h-bonds.cc: In member function 'int coot::h_bonds::mark_donors_and_acceptors(int, int, CMMDBManager*, const coot::protein_geometry&)':
coot-h-bonds.cc:609:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_sel_1_atoms; i++) { 
                             ^
coot-h-bonds.cc:623:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_sel_2_atoms; i++) { 
                                ^
coot-coord-utils.cc: In function 'void coot::util::mutate_base(CResidue*, CResidue*, bool, bool)':
coot-coord-utils.cc:5251:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int i=0; i<n_residue_atoms; i++) { 
                              ^
coot-coord-utils.cc:5310:12: warning: unused variable 'n_atoms_new' [-Wunused-variable]
        int n_atoms_new = residue->AddAtom(at);
            ^
coot-coord-utils.cc: In function 'void coot::util::move_hetgroups_around_protein(CMMDBManager*)':
coot-coord-utils.cc:6163:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                   ^
coot-coord-utils.cc:6147:8: warning: unused variable 'n_atoms' [-Wunused-variable]
    int n_atoms = residue_p->GetNumberOfAtoms();
        ^
coot-coord-utils.cc:6144:15: warning: unused variable 'at' [-Wunused-variable]
        CAtom *at = 0;
               ^
coot-coord-utils.cc: In function 'clipper::Mat33<> coot::util::residue_orientation(CResidue*, const clipper::Mat33<>&)':
coot-coord-utils.cc:6376:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++) {
                                ^
coot-coord-utils.cc: In constructor 'coot::position_residue_by_internal_coordinates::position_residue_by_internal_coordinates(CResidue*, CResidue*, const coot::atom_name_quad&, const double&, const double&, const double&)':
coot-coord-utils.cc:6782:9: warning: unused variable 'status' [-Wunused-variable]
    bool status = 0;
         ^
coot-coord-utils.cc: In member function 'CAtom* coot::position_residue_by_internal_coordinates::get_atom(CResidue*, CResidue*, const coot::atom_name_quad&, int)':
coot-coord-utils.cc:6834:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o read-sm-cif.lo read-sm-cif.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c read-sm-cif.cc  -fPIC -DPIC -o .libs/read-sm-cif.o
read-sm-cif.cc: In member function 'std::vector<CAtom*> coot::smcif::read_coordinates(PCMMCIFData, const clipper::Cell&, const clipper::Spacegroup&) const':
read-sm-cif.cc:149:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int il=0; il<ll; il++) {
                              ^
read-sm-cif.cc:145:12: warning: unused variable 'x' [-Wunused-variable]
   realtype x,y,z;
            ^
read-sm-cif.cc:145:14: warning: unused variable 'y' [-Wunused-variable]
   realtype x,y,z;
              ^
read-sm-cif.cc:145:16: warning: unused variable 'z' [-Wunused-variable]
   realtype x,y,z;
                ^
read-sm-cif.cc:210:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int il=0; il<ll; il++) {
                                  ^
read-sm-cif.cc:134:9: warning: unused variable 'S' [-Wunused-variable]
    pstr S = NULL;
         ^
read-sm-cif.cc: In member function 'CMMDBManager* coot::smcif::read_sm_cif(const string&) const':
read-sm-cif.cc:325:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int il=0; il<ll; il++) {
                                    ^
read-sm-cif.cc: In member function 'clipper::Resolution coot::smcif::get_resolution(const clipper::Cell&, const string&) const':
read-sm-cif.cc:417:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int il=0; il<ll; il++) {
                                 ^
read-sm-cif.cc:399:9: warning: unused variable 'S' [-Wunused-variable]
    pstr S = NULL;
         ^
read-sm-cif.cc: In member function 'void coot::smcif::setup_hkls(const string&)':
read-sm-cif.cc:493:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int il=0; il<ll; il++) {
                                 ^
read-sm-cif.cc:486:27: warning: unused variable 'f_sigf_input' [-Wunused-variable]
   clipper::HKL_data_base* f_sigf_input;
                           ^
read-sm-cif.cc:491:18: warning: unused variable 'x1' [-Wunused-variable]
   clipper::xtype x1[2]; 
                  ^
read-sm-cif.cc: In member function 'bool coot::smcif::read_data_sm_cif(const string&)':
read-sm-cif.cc:576:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int il=0; il<ll; il++) {
                                   ^
read-sm-cif.cc:568:29: warning: unused variable 'f_sigf_input' [-Wunused-variable]
     clipper::HKL_data_base* f_sigf_input;
                             ^
read-sm-cif.cc: In member function 'std::pair<bool, clipper::Spacegroup> coot::smcif::get_space_group(PCMMCIFData, const string&) const':
read-sm-cif.cc:747:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int il=0; il<ll; il++) {
                              ^
read-sm-cif.cc:748:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int itag=0; itag<n_tags; itag++) { 
                                     ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o bonded-pairs.lo bonded-pairs.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c bonded-pairs.cc  -fPIC -DPIC -o .libs/bonded-pairs.o
bonded-pairs.cc: In member function 'void coot::bonded_pair_t::delete_atom(CResidue*, const string&)':
bonded-pairs.cc:129:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                 ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o helix-analysis.lo helix-analysis.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c helix-analysis.cc  -fPIC -DPIC -o .libs/helix-analysis.o
helix-analysis.cc: In member function 'void coot::helix_params_container_t::make(CMMDBManager*, std::string, int, int)':
helix-analysis.cc:20:10: warning: unused variable 'at' [-Wunused-variable]
   CAtom *at;
          ^
helix-analysis.cc: In member function 'void coot::helix_params_t::calc_B()':
helix-analysis.cc:124:14: warning: unused variable 'd_sin_theta' [-Wunused-variable]
       double d_sin_theta = clipper::Coord_orth::dot(B, c_crossed)/(len_C*len_C);
              ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o elastic.lo elastic.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c elastic.cc  -fPIC -DPIC -o .libs/elastic.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-shelx-ins.lo coot-shelx-ins.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-shelx-ins.cc  -fPIC -DPIC -o .libs/coot-shelx-ins.o
elastic.cc: In constructor 'coot::elastic_network_model_t::elastic_network_model_t(CMMDBManager*, int, realtype, realtype, int)':
elastic.cc:42:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i=0; i<n_contacts; i++) { 
                                  ^
elastic.cc:54:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (contact_indices.size() < max_n_distances) {
                                         ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-coord-extras.lo coot-coord-extras.cc
In file included from coot-shelx-ins.cc:31:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-shelx-ins.cc: In constructor 'coot::ShelxIns::ShelxIns(const string&)':
coot-shelx-ins.cc:46:33: warning: variable 'p' set but not used [-Wunused-but-set-variable]
    coot::shelx_read_file_info_t p =
                                 ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-coord-extras.cc  -fPIC -DPIC -o .libs/coot-coord-extras.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-coord-lsq.lo coot-coord-lsq.cc
coot-shelx-ins.cc: In member function 'coot::shelx_read_file_info_t coot::ShelxIns::read_file(const string&)':
coot-shelx-ins.cc:94:17: warning: variable 'in_residue_flag' set but not used [-Wunused-but-set-variable]
       short int in_residue_flag = 0;
                 ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-tree-extras.lo coot-tree-extras.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-coord-lsq.cc  -fPIC -DPIC -o .libs/coot-coord-lsq.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-tree-extras.cc  -fPIC -DPIC -o .libs/coot-tree-extras.o
In file included from coot-coord-extras.cc:31:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-coord-lsq.cc:23:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-coord-lsq.cc: In function 'std::pair<std::vector<clipper::Coord_orth>, std::vector<clipper::Coord_orth> > coot::util::get_matching_indices(CMMDBManager*, CMMDBManager*, const coot::lsq_range_match_info_t&, int)':
coot-coord-lsq.cc:291:15: warning: variable 'found_atom2' set but not used [-Wunused-but-set-variable]
     short int found_atom2 = 0;
               ^
coot-coord-lsq.cc:324:15: warning: unused variable 'found_atom2' [-Wunused-variable]
     short int found_atom2 = 0;
               ^
In file included from coot-tree-extras.cc:28:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-coord-extras.cc: In function 'CResidue* coot::GetResidue(const coot::minimol::residue&)':
coot-coord-extras.cc:93:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int ic=0; ic<new_length; ic++)
                                  ^
coot-coord-extras.cc: In member function 'std::pair<bool, double> coot::match_torsions::apply_torsion_by_contacts(const coot::atom_name_quad&, const coot::atom_name_quad&, const string&)':
coot-coord-extras.cc:580:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (wiggled_ligand_residue.atoms.size() <= n_residue_atoms) { 
                                                  ^
coot-coord-extras.cc: In function 'std::vector<std::pair<CAtom*, CAtom*> > coot::torsionable_bonds_monomer_internal(CResidue*, PPCAtom, int, bool, coot::protein_geometry*)':
coot-coord-extras.cc:636:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat1=0; iat1<n_selected_atoms; iat1++) {
                                     ^
coot-coord-extras.cc:639:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int iat2=0; iat2<n_selected_atoms; iat2++) {
                                        ^
coot-coord-extras.cc: In function 'std::vector<coot::torsion_atom_quad> coot::torsionable_bonds_monomer_internal_quads(CResidue*, PPCAtom, int, bool, coot::protein_geometry*)':
coot-coord-extras.cc:699:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int iat=0; iat<n_selected_atoms; iat++) {
                                      ^
coot-coord-extras.cc: In function 'coot::bonded_pair_container_t coot::linkrs_in_atom_selection(CMMDBManager*, PPCAtom, int, coot::protein_geometry*)':
coot-coord-extras.cc:736:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_selected_atoms; i++) {
                             ^
coot-coord-extras.cc:748:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ilink=0; ilink<n_linkrs; ilink++) { 
                                     ^
coot-tree-extras.cc: In constructor 'coot::atom_tree_t::atom_tree_t(const std::vector<std::vector<int> >&, int, CMMDBManager*, int)':
coot-tree-extras.cc:79:9: warning: unused variable 'r' [-Wunused-variable]
    bool r = fill_atom_vertex_vec_using_contacts_by_atom_selection(contact_indices,
         ^
coot-tree-extras.cc: In member function 'void coot::atom_tree_t::construct_internal(const coot::dictionary_residue_restraints_t&, CResidue*, const string&)':
coot-tree-extras.cc:176:9: warning: unused variable 'success_torsion' [-Wunused-variable]
    bool success_torsion = fill_torsions(rest, res, altconf); 
         ^
coot-tree-extras.cc: In member function 'bool coot::atom_tree_t::fill_torsions(const coot::dictionary_residue_restraints_t&, CResidue*, const string&)':
coot-tree-extras.cc:229:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (iv == quads[iquad].index2) {
                             ^
coot-tree-extras.cc: In member function 'bool coot::atom_tree_t::fill_atom_vertex_vec(const coot::dictionary_residue_restraints_t&, CResidue*, const string&)':
coot-tree-extras.cc:461:8: warning: variable 'rest_tree_start_index' set but not used [-Wunused-but-set-variable]
    int rest_tree_start_index = -1;
        ^
coot-tree-extras.cc: In member function 'std::pair<int, std::vector<coot::map_index_t> > coot::atom_tree_t::get_forward_atoms(const coot::map_index_t&, const coot::map_index_t&) const':
coot-tree-extras.cc:1019:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (index.index() >= atom_vertex_vec.size())
                                              ^
coot-tree-extras.cc: In member function 'std::vector<coot::map_index_t> coot::atom_tree_t::complementary_indices(const std::vector<coot::map_index_t>&, const coot::map_index_t&, const coot::map_index_t&) const':
coot-tree-extras.cc:1114:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (moving_atom_indices[im].index() == ivert) {
                                          ^
coot-tree-extras.cc:1120:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (index2.index() != ivert)
                         ^
coot-tree-extras.cc:1121:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (index3.index() != ivert)
                            ^
coot-tree-extras.cc: In member function 'coot::map_index_t coot::atom_tree_t::get_index(CAtom*) const':
coot-tree-extras.cc:1372:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
coot-tree-extras.cc:1380:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_selected_atoms; iat++) {
                                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o water-coordination.lo water-coordination.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c water-coordination.cc  -fPIC -DPIC -o .libs/water-coordination.o
In file included from water-coordination.cc:23:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lsq-improve.lo lsq-improve.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lsq-improve.cc  -fPIC -DPIC -o .libs/lsq-improve.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-coord-utils-glyco.lo coot-coord-utils-glyco.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-coord-utils-glyco.cc  -fPIC -DPIC -o .libs/coot-coord-utils-glyco.o
In file included from lsq-improve.hh:21:0,
                 from lsq-improve.cc:29:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
lsq-improve.cc: In member function 'void coot::lsq_improve::improve()':
lsq-improve.cc:149:8: warning: unused variable 'found_match_before' [-Wunused-variable]
   bool found_match_before = 0;
        ^
lsq-improve.cc: In member function 'std::vector<coot::lsq_range_match_info_t> coot::lsq_improve::get_new_matches(const std::map<coot::residue_spec_t, std::vector<coot::residue_spec_t> >&) const':
lsq-improve.cc:313:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (contiguous_frag_spec.size() >= n_res_for_frag) {
                                            ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-map-utils.lo coot-map-utils.cc
In file included from coot-coord-extras.hh:30:0,
                 from coot-coord-utils-glyco.cc:26:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-map-utils.cc  -fPIC -DPIC -o .libs/coot-map-utils.o
coot-coord-utils-glyco.cc: In member function 'CResidue* coot::beam_in_linked_residue::get_residue() const':
coot-coord-utils-glyco.cc:341:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i=0; i<n_residue_atoms; i++) {
                               ^
coot-coord-utils-glyco.cc: In member function 'void coot::beam_in_linked_residue::delete_atom(CResidue*, const string&) const':
coot-coord-utils-glyco.cc:512:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                 ^
coot-coord-utils-glyco.cc:529:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                 ^
coot-coord-utils-glyco.cc:530:14: warning: unused variable 'at' [-Wunused-variable]
       CAtom *at = residue_atoms[iat];
              ^
coot-coord-utils-glyco.cc: In member function 'std::vector<CAtom*> coot::beam_in_linked_residue::get_atoms(CResidue*, const std::vector<std::basic_string<char> >&) const':
coot-coord-utils-glyco.cc:556:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
coot-coord-utils-glyco.cc: In member function 'CResidue* coot::beam_in_linked_residue::get_residue(const string&, CMMDBManager*) const':
coot-coord-utils-glyco.cc:624:14: warning: unused variable 'at' [-Wunused-variable]
       CAtom *at;
              ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o peak-search.lo peak-search.cc
In file included from coot-map-utils.hh:29:0,
                 from coot-map-utils.cc:34:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-map-utils.cc: In function 'clipper::Xmap<float> coot::util::reinterp_map_fine_gridding(const clipper::Xmap<float>&)':
coot-map-utils.cc:171:23: warning: variable 'cg_old' set but not used [-Wunused-but-set-variable]
   clipper::Coord_grid cg_old = cf.coord_grid(gs_old);
                       ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c peak-search.cc  -fPIC -DPIC -o .libs/peak-search.o
coot-map-utils.cc: In member function 'std::pair<int, clipper::Xmap<int> > coot::util::segment_map::segment_emsley_flood(const clipper::Xmap<float>&, float)':
coot-map-utils.cc:797:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i_n=0; i_n<neighb.size(); i_n++) {
                                               ^
coot-map-utils.cc:809:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int i_nn=0; i_nn<neighb.size(); i_nn++) {
                                                   ^
coot-map-utils.cc: In member function 'std::pair<int, clipper::Xmap<int> > coot::util::segment_map::segment(const clipper::Xmap<float>&, float)':
coot-map-utils.cc:883:9: warning: unused variable 'v' [-Wunused-variable]
   float v = xmap[density_values[i].first];
         ^
coot-map-utils.cc: In member function 'void coot::util::segment_map::resegment_watershed_points(clipper::Xmap<int>*, const clipper::Xmap<float>&) const':
coot-map-utils.cc:968:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i_n=0; i_n<neighb.size(); i_n++) {
                                            ^
coot-map-utils.cc:981:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i_n=0; i_n<neighb.size(); i_n++) {
                                               ^
coot-map-utils.cc: In member function 'std::pair<int, clipper::Xmap<int> > coot::util::segment_map::segment(const clipper::Xmap<float>&, float, float, int)':
coot-map-utils.cc:1196:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int icount=0; icount<segment_vec.size(); icount++) {
                                               ^
coot-map-utils.cc: In member function 'void coot::util::segment_map::flood_fill_segmented_map(clipper::Xmap<std::pair<bool, int> >*, const clipper::Xmap<float>&, const clipper::Coord_grid&, int, int)':
coot-map-utils.cc:1305:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i_n=0; i_n<neighb.size(); i_n++) {
                                                ^
coot-map-utils.cc:1327:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i_n=0; i_n<neighb.size(); i_n++) {
                                                ^
coot-map-utils.cc: In member function 'std::vector<clipper::Coord_grid> coot::util::segment_map::path_to_peak(const clipper::Coord_grid&, const clipper::Xmap<float>&)':
coot-map-utils.cc:1359:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i_n=0; i_n<neighb.size(); i_n++) {
                                                ^
coot-map-utils.cc: In function 'clipper::Xmap<float> coot::util::calc_atom_map(CMMDBManager*, int, const clipper::Cell&, const clipper::Spacegroup&, const clipper::Grid_sampling&)':
coot-map-utils.cc:1405:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_atoms; i++) {
                             ^
coot-map-utils.cc: In function 'float coot::util::map_to_model_correlation(CMMDBManager*, const std::vector<coot::residue_spec_t>&, short unsigned int, float, const clipper::Xmap<float>&)':
coot-map-utils.cc:1511:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_atoms; iat++) {
                                    ^
coot-map-utils.cc: In function 'std::vector<std::pair<coot::residue_spec_t, float> > coot::util::map_to_model_correlation_per_residue(CMMDBManager*, const std::vector<coot::residue_spec_t>&, short unsigned int, float, const clipper::Xmap<float>&)':
coot-map-utils.cc:1674:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_atoms; iat++) {
                                    ^
peak-search.cc: In member function 'void coot::peak_search::peak_search_0(const clipper::Xmap<float>&, clipper::Xmap<short int>*, float) const':
peak-search.cc:219:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int i=0; i<neighb.size(); i++) {
                                          ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o peak-search-from-list.lo peak-search-from-list.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c peak-search-from-list.cc  -fPIC -DPIC -o .libs/peak-search-from-list.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o trim.lo trim.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c trim.cc  -fPIC -DPIC -o .libs/trim.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o xmap-stats.lo xmap-stats.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c xmap-stats.cc  -fPIC -DPIC -o .libs/xmap-stats.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-map-heavy.lo coot-map-heavy.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-fffear.lo coot-fffear.cc
In file included from coot-map-utils.hh:29:0,
                 from trim.cc:21:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-map-heavy.cc  -fPIC -DPIC -o .libs/coot-map-heavy.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-fffear.cc  -fPIC -DPIC -o .libs/coot-fffear.o
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-h-bonds.o test-h-bonds.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-shelx-reader.o test-shelx-reader.cc
In file included from coot-h-bonds.hh:12:0,
                 from test-h-bonds.cc:7:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-map-utils.hh:29:0,
                 from coot-map-heavy.cc:29:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-map-utils.hh:29:0,
                 from coot-fffear.cc:30:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-fffear.cc: In constructor 'coot::util::fffear_search::fffear_search(CMMDBManager*, int, const clipper::Xmap<float>&, float, bool)':
coot-fffear.cc:86:24: warning: variable 'low_left' set but not used [-Wunused-but-set-variable]
    clipper::Coord_orth low_left = e.first;
                        ^
coot-fffear.cc:132:8: warning: unused variable 'npoints2' [-Wunused-variable]
    int npoints2 = fill_nxmap_mask(mol, SelectionHandle, mid_point_);
        ^
coot-map-heavy.cc: In function 'int coot::util::fit_to_map_by_simplex_rigid(PPCAtom, int, const clipper::Xmap<float>&)':
coot-map-heavy.cc:53:11: warning: variable 'ssval' set but not used [-Wunused-but-set-variable]
    double ssval;
           ^
coot-map-heavy.cc: In function 'std::vector<std::pair<std::basic_string<char>, float> > coot::util::score_atoms(const coot::minimol::residue&, const clipper::Xmap<float>&)':
coot-map-heavy.cc:313:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<residue.n_atoms(); i++) { 
                                             ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-utils.o test-utils.cc
In file included from test-utils.cc:27:0:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-hole.o test-hole.cc
test-utils.cc: In function 'int test_glyco_tree()':
test-utils.cc:263:8: warning: unused variable 'dynamic_add_status_1' [-Wunused-variable]
    int dynamic_add_status_1 = t.geom.try_dynamic_add("NAG", 1);
        ^
test-utils.cc:264:8: warning: unused variable 'dynamic_add_status_2' [-Wunused-variable]
    int dynamic_add_status_2 = t.geom.try_dynamic_add("MAN", 1);
        ^
test-utils.cc:265:8: warning: unused variable 'dynamic_add_status_3' [-Wunused-variable]
    int dynamic_add_status_3 = t.geom.try_dynamic_add("BMA", 1);
        ^
test-utils.cc:266:8: warning: unused variable 'dynamic_add_status_4' [-Wunused-variable]
    int dynamic_add_status_4 = t.geom.try_dynamic_add("GAL", 1);
        ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-elastic.o test-elastic.cc
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-coord-utils.la -rpath /usr/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o .libs/coot-h-bonds.o .libs/hole.o .libs/read-sm-cif.o .libs/bonded-pairs.o .libs/helix-analysis.o .libs/elastic.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0
test-elastic.cc: In function 'int main(int, char**)':
test-elastic.cc:43:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) { 
                                ^
libtool: link: (cd ".libs" && rm -f "libcoot-coord-utils.so.0" && ln -s "libcoot-coord-utils.so.0.0.0" "libcoot-coord-utils.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-coord-utils.so" && ln -s "libcoot-coord-utils.so.0.0.0" "libcoot-coord-utils.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-coord-utils.la" && ln -s "../libcoot-coord-utils.la" "libcoot-coord-utils.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-shelx.la -rpath /usr/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la 
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXCircle.lo CXXCircle.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXSphereTriangle.lo CXXSphereTriangle.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSphereElement.cpp  -fPIC -DPIC -o .libs/CXXSphereElement.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSphereNode.cpp  -fPIC -DPIC -o .libs/CXXSphereNode.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXChargeTable.cpp  -fPIC -DPIC -o .libs/CXXChargeTable.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXCircle.cpp  -fPIC -DPIC -o .libs/CXXCircle.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSphereTriangle.cpp  -fPIC -DPIC -o .libs/CXXSphereTriangle.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXCircleNode.lo CXXCircleNode.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXCircleNode.cpp  -fPIC -DPIC -o .libs/CXXCircleNode.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXSphereTriangleEdge.lo CXXSphereTriangleEdge.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSphereTriangleEdge.cpp  -fPIC -DPIC -o .libs/CXXSphereTriangleEdge.o
CXXCircleNode.cpp: In static member function 'static int CXXCircleNode::probeContacts(std::vector<CXXCircleNode, CXX::CXXAlloc<CXXCircleNode> >&, double, std::map<CXXCircleNode*, std::vector<CXXCircleNode*, CXX::CXXAlloc<CXXCircleNode*> > >&)':
CXXCircleNode.cpp:161:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int iCentralProbe = 0; iCentralProbe < centralBin.size(); iCentralProbe++){
                                                                             ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXCoord.lo CXXCoord.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXCoord.cpp  -fPIC -DPIC -o .libs/CXXCoord.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXSurface.lo CXXSurface.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSurface.cpp  -fPIC -DPIC -o .libs/CXXSurface.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXCreator.lo CXXCreator.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXCreator.cpp  -fPIC -DPIC -o .libs/CXXCreator.o
CXXSurface.cpp: In member function 'int CXXSurface::calculateVDWFromAtoms(PCMMDBManager, int, int, double, double, bool)':
CXXSurface.cpp:496:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<vdwBallPntrs.size(); i++){
                                    ^
CXXSurface.cpp:497:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete vdwBallPntrs[i];
                                             ^
CXXSurface.cpp:499:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<contextBallPntrs.size(); i++){
                                        ^
CXXSurface.cpp:502:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
    if (contextBallPntrs[i]) delete contextBallPntrs[i];
                                                      ^
CXXSurface.cpp: In member function 'int CXXSurface::calculateAccessibleFromAtoms(PCMMDBManager, int, int, double, double, bool)':
CXXSurface.cpp:548:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<vdwBallPntrs.size(); i++){
                                    ^
CXXSurface.cpp:549:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete vdwBallPntrs[i];
                                             ^
CXXSurface.cpp:551:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<contextBallPntrs.size(); i++){
                                        ^
CXXSurface.cpp:554:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
    if (contextBallPntrs[i]) delete contextBallPntrs[i];
                                                      ^
CXXSurface.cpp: In member function 'int CXXSurface::calculateFromAtoms(PCMMDBManager, int, int, double, double, bool)':
CXXSurface.cpp:633:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<vdwBallPntrs.size(); i++){
                                       ^
CXXSurface.cpp:634:79: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete static_cast<const CXXAtomBall *>(vdwBallPntrs[i]);
                                                                               ^
CXXSurface.cpp:636:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<contextBallPntrs.size(); i++){
                                        ^
CXXSurface.cpp:637:87: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (contextBallPntrs[i]) delete static_cast<const CXXAtomBall *>(contextBallPntrs[i]);
                                                                                       ^
CXXSurface.cpp:640:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<reentrantProbes.size(); i++){
                                       ^
CXXSurface.cpp:641:71: warning: deleting object of polymorphic class type 'CXXReentrantProbeBall' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
   delete static_cast<const CXXReentrantProbeBall *>(reentrantProbes[i]);
                                                                       ^
CXXSurface.cpp: In member function 'int CXXSurface::getPointer(const string&, int, void**)':
CXXSurface.cpp:1127:9: warning: variable 'relevantVector' set but not used [-Wunused-but-set-variable]
     int relevantVector;
         ^
CXXSurface.cpp: In member function 'void CXXSurface::compress(double)':
CXXSurface.cpp:1179:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<vertices.size(); i++){
                                ^
CXXSurface.cpp:1181:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j<compressedVertices.size() && uniqueAndDrawn; j++){
                                           ^
CXXSurface.cpp:1197:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<triangles.size(); i++){
                                 ^
CXXCreator.cpp: In member function 'int CXXCreator::addAtomSolvationParameters()':
CXXCreator.cpp:658:9: warning: variable 'theAtomRadius' set but not used [-Wunused-but-set-variable]
  double theAtomRadius;
         ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXSurfaceVertex.lo CXXSurfaceVertex.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSurfaceVertex.cpp  -fPIC -DPIC -o .libs/CXXSurfaceVertex.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXException.lo CXXException.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXException.cpp  -fPIC -DPIC -o .libs/CXXException.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXTorusElement.lo CXXTorusElement.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXFFTSolventMap.lo CXXFFTSolventMap.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXTorusElement.cpp  -fPIC -DPIC -o .libs/CXXTorusElement.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXFFTSolventMap.cpp  -fPIC -DPIC -o .libs/CXXFFTSolventMap.o
CXXTorusElement.cpp: In constructor 'CXXTorusElement::CXXTorusElement(const CXXCircle&, int, double, double)':
CXXTorusElement.cpp:68:6: warning: variable 'tooSmallTorus' set but not used [-Wunused-but-set-variable]
  int tooSmallTorus = 0;
      ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXTorusNode.lo CXXTorusNode.cpp
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libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXTorusNode.cpp  -fPIC -DPIC -o .libs/CXXTorusNode.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXFortranFile.cpp  -fPIC -DPIC -o .libs/CXXFortranFile.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXNewHood.lo CXXNewHood.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXNewHood.cpp  -fPIC -DPIC -o .libs/CXXNewHood.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXTriangle.lo CXXTriangle.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXTriangle.cpp  -fPIC -DPIC -o .libs/CXXTriangle.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXNode.lo CXXNode.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXNode.cpp  -fPIC -DPIC -o .libs/CXXNode.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXQADSurface.lo CXXQADSurface.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXBall.lo CXXBall.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXBall.cpp  -fPIC -DPIC -o .libs/CXXBall.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXQADSurface.cpp  -fPIC -DPIC -o .libs/CXXQADSurface.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXQADSurfaceStaticData.cpp  -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o
CXXBall.cpp: In static member function 'static int CXXBall::triangulateBalls(std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, double, CXXSurface*, int)':
CXXBall.cpp:58:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<raggedEdges.size(); i++){
                                   ^
CXXBall.cpp:84:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<trimmedBalls.size(); i++){
                                    ^
CXXBall.cpp: In static member function 'static int CXXBall::ballContacts(std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, std::map<const CXXBall*, std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> > >&)':
CXXBall.cpp:201:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iBall=0; iBall< balls.size(); iBall++){
                                         ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXSpace.lo CXXSpace.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXSpace.cpp  -fPIC -DPIC -o .libs/CXXSpace.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CXXUtils.lo CXXUtils.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CXXUtils.cpp  -fPIC -DPIC -o .libs/CXXUtils.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libccp4mg-surface.la -rpath /usr/lib CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXBall.lo CXXQADSurfaceStaticData.lo CXXSpace.lo CXXUtils.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXBall.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o .libs/CXXUtils.o   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -fopenmp -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libccp4mg-surface.so.0 -o .libs/libccp4mg-surface.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so.0" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so.0")
libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so")
libtool: link: ( cd ".libs" && rm -f "libccp4mg-surface.la" && ln -s "../libccp4mg-surface.la" "libccp4mg-surface.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/surface'
Making all in coot-surface
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-surface'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP       -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-surface.lo coot-surface.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP       -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rgbreps.lo rgbreps.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c rgbreps.cc  -fPIC -DPIC -o .libs/rgbreps.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-surface.cc  -fPIC -DPIC -o .libs/coot-surface.o
rgbreps.cc: In static member function 'static int RGBReps::GetColourNumber(std::string)':
rgbreps.cc:72:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0;i<colours_name_map.size();i++) {
                                        ^
rgbreps.cc: In static member function 'static std::vector<std::vector<double> > RGBReps::GetColourDefinitions(std::vector<int>, int)':
rgbreps.cc:113:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0;i< n_codes;i++) {
                            ^
rgbreps.cc:116:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (ii>colours.size()){
                           ^
In file included from coot-surface.cc:33:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-surface.cc: In member function 'void coot::surface::draw(double*, int)':
coot-surface.cc:117:9: warning: unused variable 'whiteColour' [-Wunused-variable]
   float whiteColour[] = {1.,1.,1.,1.};
         ^
In file included from coot-surface.cc:30:0:
../surface/CXXUtils.h: At global scope:
../surface/CXXUtils.h:666:13: warning: 'CXXUtils::nAtomRadii' defined but not used [-Wunused-variable]
  static int nAtomRadii = sizeof(unitedAtomRadii) / sizeof(AtomRadius);
             ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lglut  -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lGL 
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-surface.o .libs/rgbreps.o   ../surface/.libs/libccp4mg-surface.so -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lGL -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0
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libtool: link: (cd ".libs" && rm -f "libcoot-surface.so" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-surface'
Making all in lidia-core
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/lidia-core'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../mini-mol -I../utils    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-shared.lo lbg-shared.cc
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../mini-mol -I../utils    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rdkit-interface.lo rdkit-interface.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../mini-mol -I../utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lbg-molfile.cc  -fPIC -DPIC -o .libs/lbg-molfile.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../mini-mol -I../utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lbg-shared.cc  -fPIC -DPIC -o .libs/lbg-shared.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../mini-mol -I../utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c rdkit-interface.cc  -fPIC -DPIC -o .libs/rdkit-interface.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../mini-mol -I../utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lig-build.cc  -fPIC -DPIC -o .libs/lig-build.o
In file included from lig-build.cc:24:0:
lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
lig-build.cc: In static member function 'static std::vector<std::pair<lig_build::pos_t, lig_build::pos_t> > lig_build::pos_t::make_wedge_in_bond(const lig_build::pos_t&, const lig_build::pos_t&)':
lig-build.cc:57:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=1; i<=n_lines; i++) {
                              ^
In file included from lbg-molfile.hh:32:0,
                 from lbg-molfile.cc:27:
lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
lbg-molfile.cc: In member function 'void lig_build::molfile_molecule_t::read(const string&)':
lbg-molfile.cc:141:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=4; i<lines.size()  && i<(n_atoms+4); i++) {
                                                             ^
lbg-molfile.cc:168:79: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=(4+n_atoms); i<lines.size()  && i<(n_bonds+n_atoms+4); i++) {
                                                                               ^
lbg-molfile.cc:191:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (((index_1-1) >=0) && (index_1-1) < atoms.size()) { 
                                                           ^
lbg-molfile.cc:192:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (((index_2-1) >=0) && (index_2-1) < atoms.size()) { 
                                                       ^
lbg-molfile.cc:233:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int ic=0; ic<nca; ic++) {
                                ^
lbg-molfile.cc: In constructor 'lig_build::molfile_molecule_t::molfile_molecule_t(CResidue*, const coot::dictionary_residue_restraints_t&)':
lbg-molfile.cc:280:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                 ^
lbg-molfile.cc:295:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                 ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-lidia-core.la -rpath /usr/lib lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la  
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/lbg-shared.o .libs/lbg-molfile.o .libs/lig-build.o .libs/rdkit-interface.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb ../utils/.libs/libcoot-utils.so -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-lidia-core.so.0" && ln -s "libcoot-lidia-core.so.0.0.0" "libcoot-lidia-core.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-lidia-core.so" && ln -s "libcoot-lidia-core.so.0.0.0" "libcoot-lidia-core.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-lidia-core.la" && ln -s "../libcoot-lidia-core.la" "libcoot-lidia-core.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/lidia-core'
Making all in coords
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coords'
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cos-sin.lo cos-sin.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o mmdb-extras.lo mmdb-extras.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o utils.lo utils.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c Bond_lines.cc  -fPIC -DPIC -o .libs/Bond_lines.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mmdb-extras.cc  -fPIC -DPIC -o .libs/mmdb-extras.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c utils.cc  -fPIC -DPIC -o .libs/utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c cos-sin.cc  -fPIC -DPIC -o .libs/cos-sin.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c Cartesian.cc  -fPIC -DPIC -o .libs/Cartesian.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o mmdb.lo mmdb.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mmdb.cc  -fPIC -DPIC -o .libs/mmdb.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o mmdb-crystal.lo mmdb-crystal.cc
Cartesian.cc: In static member function 'static double coot::Cartesian::DihedralAngle(const coot::Cartesian&, const coot::Cartesian&, const coot::Cartesian&, const coot::Cartesian&)':
Cartesian.cc:419:20: warning: variable 'v3b' set but not used [-Wunused-but-set-variable]
    coot::Cartesian v3b= c - d; // backwards
                    ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mmdb-crystal.cc  -fPIC -DPIC -o .libs/mmdb-crystal.o
In file included from mmdb-extras.cc:30:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o Bond_lines_ext.lo Bond_lines_ext.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from mmdb.h:25,
                 from mmdb.cc:40:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c Bond_lines_ext.cc  -fPIC -DPIC -o .libs/Bond_lines_ext.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from mmdb.h:25,
                 from mmdb-extras.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from mmdb.cc:43:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
mmdb-extras.cc: In function 'atom_selection_container_t make_asc(CMMDBManager*)':
mmdb-extras.cc:146:8: warning: unused variable 'nSelAtoms' [-Wunused-variable]
    int nSelAtoms;
        ^
mmdb-extras.cc: In function 'CResidue* coot::deep_copy_this_residue(CResidue*, const string&, short int, int, bool)':
mmdb-extras.cc:218:9: warning: unused variable 'i_add' [-Wunused-variable]
     int i_add = rres->AddAtom(atom_p);
         ^
mmdb-extras.cc: In function 'std::pair<CResidue*, atom_selection_container_t> coot::deep_copy_this_residue_and_make_asc(CMMDBManager*, CResidue*, const string&, short int, int, int)':
mmdb-extras.cc:299:10: warning: unused variable 'i_add' [-Wunused-variable]
      int i_add = rres->AddAtom(atom_p);
          ^
mmdb-extras.cc:288:14: warning: variable 'do_shelx_afix_data_flag' set but not used [-Wunused-but-set-variable]
    short int do_shelx_afix_data_flag = 0;
              ^
mmdb-extras.cc: In constructor 'coot::contact_info::contact_info(const atom_selection_container_t&, const string&, coot::protein_geometry*)':
mmdb-extras.cc:387:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<asc.n_selected_atoms; i++) {
                                    ^
mmdb-extras.cc: In constructor 'coot::contact_info::contact_info(const atom_selection_container_t&, coot::protein_geometry*, const coot::bonded_pair_container_t&)':
mmdb-extras.cc:417:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<asc.n_selected_atoms; i++) {
                                 ^
mmdb-extras.cc: In member function 'void coot::contact_info::contacts_from_monomer_restraints(atom_selection_container_t, std::map<CResidue*, coot::dictionary_residue_restraints_t>&)':
mmdb-extras.cc:509:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<asc.n_selected_atoms; iat++) {
                                     ^
mmdb-extras.cc:512:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int jat=0; jat<asc.n_selected_atoms; jat++) {
                                        ^
mmdb-extras.cc: In member function 'void coot::contact_info::setup_from_monomer_restraints(const atom_selection_container_t&, coot::protein_geometry*)':
mmdb-extras.cc:551:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<asc.n_selected_atoms; i++) {
                                 ^
mmdb-extras.cc: In constructor 'coot::contact_info::contact_info(const atom_selection_container_t&, coot::protein_geometry*, const std::vector<std::pair<CAtom*, CAtom*> >&)':
mmdb-extras.cc:582:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<asc.n_selected_atoms; i++) {
                                    ^
mmdb-extras.cc:584:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int j=0; j<asc.n_selected_atoms; j++) {
                                   ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from mmdb.h:25,
                 from Bond_lines.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from mmdb.h:25,
                 from mmdb-crystal.cc:45:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from Bond_lines.cc:40:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
Bond_lines.cc: In member function 'clipper::Coord_orth Bond_lines_container::get_neighb_normal(int, int, PPCAtom, int, bool) const':
Bond_lines.cc:669:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int j=0; j<n_atoms; j++) {
                               ^
Bond_lines.cc: In member function 'bool Bond_lines_container::invert_deloc_bond_displacement_vector(const clipper::Coord_orth&, int, int, PPCAtom, int, const std::vector<coot::dict_bond_restraint_t>&) const':
Bond_lines.cc:735:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_atoms; iat++)
                                 ^
mmdb-crystal.cc: In member function 'std::vector<std::pair<symm_trans_t, Cell_Translation> > molecule_extents_t::which_boxes(coot::Cartesian, atom_selection_container_t, int) const':
mmdb-crystal.cc:294:25: warning: unused variable 'u_cs' [-Wunused-variable]
       realtype u, v, w, u_cs, v_cs, w_cs;
                         ^
mmdb-crystal.cc:294:31: warning: unused variable 'v_cs' [-Wunused-variable]
       realtype u, v, w, u_cs, v_cs, w_cs;
                               ^
mmdb-crystal.cc:294:37: warning: unused variable 'w_cs' [-Wunused-variable]
       realtype u, v, w, u_cs, v_cs, w_cs;
                                     ^
Bond_lines.cc: In member function 'void Bond_lines_container::add_bonds_het_residues(const std::vector<std::pair<bool, CResidue*> >&, int, short int, int)':
Bond_lines.cc:838:10: warning: variable 'added_bond' set but not used [-Wunused-but-set-variable]
     bool added_bond = 0; 
          ^
mmdb-crystal.cc: In member function 'std::vector<std::pair<int, symm_trans_t> > molecule_extents_t::which_strict_ncs(const coot::Cartesian&, atom_selection_container_t&, const std::vector<coot::coot_mat44>&, const Cell_Translation&) const':
mmdb-crystal.cc:432:46: warning: variable 'u_cs' set but not used [-Wunused-but-set-variable]
    realtype diff_x, diff_y, diff_z, u, v, w, u_cs, v_cs, w_cs;
                                              ^
Bond_lines.cc: In member function 'void Bond_lines_container::add_aromatic_ring_bond_lines(const std::vector<std::basic_string<char> >&, CResidue*, int)':
Bond_lines.cc:993:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                ^
mmdb-crystal.cc:432:52: warning: variable 'v_cs' set but not used [-Wunused-but-set-variable]
    realtype diff_x, diff_y, diff_z, u, v, w, u_cs, v_cs, w_cs;
                                                    ^
Bond_lines.cc:1028:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int istep=0; istep<n_steps; istep++) {
                                       ^
mmdb-crystal.cc:432:58: warning: variable 'w_cs' set but not used [-Wunused-but-set-variable]
    realtype diff_x, diff_y, diff_z, u, v, w, u_cs, v_cs, w_cs;
                                                          ^
Bond_lines.cc: In member function 'CAtom** coot::model_bond_atom_info_t::Hydrogen_atoms() const':
Bond_lines.cc:1227:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<hydrogen_atoms_.size(); i++) {
                                         ^
Bond_lines.cc: In member function 'CAtom** coot::model_bond_atom_info_t::non_Hydrogen_atoms() const':
Bond_lines.cc:1237:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<non_hydrogen_atoms_.size(); i++) {
                                             ^
mmdb-crystal.cc: In function 'coot::Cartesian translate_atom_with_pre_shift(atom_selection_container_t, int, const std::pair<symm_trans_t, Cell_Translation>&)':
mmdb-crystal.cc:1029:8: warning: unused variable 'err2' [-Wunused-variable]
    int err2 = AtomSel.mol->GetTMatrix(pre_shift_matt, 0,
        ^
Bond_lines.cc: In member function 'graphical_bonds_container Bond_lines_container::addSymmetry_whole_chain(const atom_selection_container_t&, const coot::Cartesian&, float, const std::vector<std::pair<symm_trans_t, Cell_Translation> >&)':
Bond_lines.cc:2045:10: warning: variable 'identity_matt' set but not used [-Wunused-but-set-variable]
    mat44 identity_matt;
          ^
Bond_lines.cc: In member function 'graphical_bonds_container Bond_lines_container::addSymmetry_calphas(const atom_selection_container_t&, const coot::Cartesian&, float, const std::vector<std::pair<symm_trans_t, Cell_Translation> >&)':
Bond_lines.cc:2311:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int iat=0; iat<ca_this.size(); iat++) { 
                                         ^
Bond_lines.cc:2313:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int jat=0; jat<ca_next.size(); jat++) { 
                                     ^
Bond_lines.cc: In member function 'graphical_bonds_container Bond_lines_container::add_NCS_molecule(const atom_selection_container_t&, const coot::Cartesian&, float, const std::pair<coot::coot_mat44, symm_trans_t>&, short int, short int)':
Bond_lines.cc:2383:10: warning: variable 'm' set but not used [-Wunused-but-set-variable]
    mat44 m;
          ^
Bond_lines.cc: In member function 'atom_selection_container_t Bond_lines_container::ContactSel(PPCAtom, PSContact, int) const':
Bond_lines.cc:2508:13: warning: unused variable 'last_id2' [-Wunused-variable]
    int id2, last_id2 = -1;
             ^
Bond_lines.cc: In member function 'int Bond_lines_container::set_rainbow_colours(CMMDBManager*)':
Bond_lines.cc:3339:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int iat=0; iat<n_atoms; iat++) { 
                                     ^
Bond_lines.cc: In member function 'void Bond_lines_container::do_colour_sec_struct_bonds(const atom_selection_container_t&, float, float)':
Bond_lines.cc:3655:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int imodel=0; imodel<n_models; imodel++) { 
                                          ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-close.lo coot-close.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-close.cc  -fPIC -DPIC -o .libs/coot-close.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la  -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../geometry/.libs/libcoot-geometry.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-coords.so.0" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-coords.so" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coords'
Making all in angles
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/angles'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -I/usr/include/mmdb -I/usr/include/ssm -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o libcoot_AngleInfo_la-AngleInfo.lo `test -f 'AngleInfo.cc' || echo './'`AngleInfo.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -I/usr/include/mmdb -I/usr/include/ssm -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo `test -f 'AngleInfo-angle-torsions-autogen.cc' || echo './'`AngleInfo-angle-torsions-autogen.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.   -I/usr/include/mmdb -I/usr/include/ssm -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo `test -f 'AngleInfo-theta_2-autogen.cc' || echo './'`AngleInfo-theta_2-autogen.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -I/usr/include/ssm -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c AngleInfo-theta_2-autogen.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -I/usr/include/ssm -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c AngleInfo-angle-torsions-autogen.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -I/usr/include/ssm -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c AngleInfo.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo.o
AngleInfo.cc: In member function 'float AngleInfo::prob_angle_torsion(float, float) const':
AngleInfo.cc:244:8: warning: unused variable 'a' [-Wunused-variable]
    int a = int (floor(angle_index));
        ^
AngleInfo.cc:245:8: warning: unused variable 't' [-Wunused-variable]
    int t = int (floor(torsion_index)); 
        ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -g -O1 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-AngleInfo.la -rpath /usr/lib libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo  
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/libcoot_AngleInfo_la-AngleInfo.o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o   -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O1 -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-AngleInfo.so.0 -o .libs/libcoot-AngleInfo.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so.0" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/angles'
Making all in skeleton
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/skeleton'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../mini-mol -I../geometry -I../coords -I../angles -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o dm-utils.lo dm-utils.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../mini-mol -I../geometry -I../coords -I../angles -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphical_skel.lo graphical_skel.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../mini-mol -I../geometry -I../coords -I../angles -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o BuildCas.lo BuildCas.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../mini-mol -I../geometry -I../coords -I../angles -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c graphical_skel.cc  -fPIC -DPIC -o .libs/graphical_skel.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../mini-mol -I../geometry -I../coords -I../angles -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c dm-utils.cc  -fPIC -DPIC -o .libs/dm-utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../mini-mol -I../geometry -I../coords -I../angles -I../coot-utils -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c BuildCas.cc  -fPIC -DPIC -o .libs/BuildCas.o
graphical_skel.cc: In member function 'graphical_bonds_container GraphicalSkel::make_graphical_bonds(const clipper::Xmap<float>&, const clipper::Xmap<int>&, coot::Cartesian, float, float) const':
graphical_skel.cc:65:24: warning: variable 'gb0' set but not used [-Wunused-but-set-variable]
    clipper::Coord_grid gb0 = iw.coord() - grid_bit;
                        ^
graphical_skel.cc:66:24: warning: variable 'gb1' set but not used [-Wunused-but-set-variable]
    clipper::Coord_grid gb1 = iw.coord() + grid_bit;
                        ^
graphical_skel.cc: In member function 'graphical_bonds_container GraphicalSkel::make_graphical_bonds(const clipper::Xmap<float>&, const clipper::Xmap<int>&) const':
graphical_skel.cc:123:8: warning: unused variable 'n_lines' [-Wunused-variable]
    int n_lines = 0;
        ^
BuildCas.cc: In member function 'small_triangle_thing BuildCas::isSmallTriangle_new(const clipper::Xmap<int>&, const clipper::Xmap<float>&, float, const clipper::Skeleton_basic::Neighbours&, const clipper::Skeleton_basic::Neighbours&, const clipper::Coord_grid&, const std::vector<coot::Cartesian>&) const':
BuildCas.cc:2090:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i_n_n = 0; i_n_n < fd_neighb.size(); i_n_n++ ) {
                                                          ^
BuildCas.cc: In member function 'void BuildCas::depth_search_skeleton_testing_2()':
BuildCas.cc:2249:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<treenodemap.get_data(ca_g_1).neighbs.size(); i++) {
                                                              ^
BuildCas.cc:2255:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<treenodemap.get_data(ca_g_2).neighbs.size(); i++) {
                                                              ^
BuildCas.cc: In member function 'short int BuildCas::depth_search_skeleton_internal(const clipper::Coord_grid&, const clipper::Coord_grid&, const clipper::Coord_grid&, const clipper::Coord_grid&, int, int) const':
BuildCas.cc:2373:23: warning: variable 'co' set but not used [-Wunused-but-set-variable]
   clipper::Coord_orth co = cf.coord_orth(d_map_p->cell()); 
                       ^
BuildCas.cc: In member function 'coot::Cartesian BuildCas::SmallTriangle_to_branch_point(const clipper::Xmap<int>&, const clipper::Skeleton_basic::Neighbours&, const clipper::Coord_grid&) const':
BuildCas.cc:2455:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int in = 0; in < fd_neighb.size(); in++ ) {
                                                  ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../angles/.libs/libcoot-AngleInfo.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so.0" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/skeleton'
Making all in ccp4mg-utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DUSE_LIBPNG  -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o geomutil.lo geomutil.cc
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DUSE_LIBPNG  -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cartesian.lo cartesian.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DUSE_LIBPNG  -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o matrix.lo matrix.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DUSE_LIBPNG  -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o quat.lo quat.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c cartesian.cc  -fPIC -DPIC -o .libs/cartesian.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c geomutil.cc  -fPIC -DPIC -o .libs/geomutil.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mgtree.cc  -fPIC -DPIC -o .libs/mgtree.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c matrix.cc  -fPIC -DPIC -o .libs/matrix.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c quat.cc  -fPIC -DPIC -o .libs/quat.o
mgtree.cc: In function 'double FindAngle(const TreeVertex*, const TreeVertex*, const TreeVertex*, const std::vector<std::vector<int> >&, const std::vector<double>&)':
mgtree.cc:153:8: warning: variable 'have_angle' set but not used [-Wunused-but-set-variable]
   bool have_angle = false;
        ^
mgtree.cc: In member function 'void Tree::SetBondsAnglesTorsions(const int&, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<std::vector<int> >&)':
mgtree.cc:734:15: warning: variable 'chiral_direction' set but not used [-Wunused-but-set-variable]
           int chiral_direction = -1;
               ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DUSE_LIBPNG  -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o ppmutil.lo ppmutil.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c ppmutil.cc  -fPIC -DPIC -o .libs/ppmutil.o
ppmutil.cc: In member function 'void image_info::readpng(const char*)':
ppmutil.cc:2510:79: warning: 'palette' may be used uninitialized in this function [-Wmaybe-uninitialized]
         pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red;
                                                                               ^
ppmutil.cc:2514:9: warning: 'num_trans' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(row_pointers[i][j]<num_trans){
         ^
ppmutil.cc:2515:86: warning: 'trans_alpha' may be used uninitialized in this function [-Wmaybe-uninitialized]
          pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
                                                                                      ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libccp4mg-utils.la -rpath /usr/lib geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo -lpng 
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/geomutil.o .libs/mgtree.o .libs/cartesian.o .libs/matrix.o .libs/quat.o .libs/ppmutil.o   -lpng -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libccp4mg-utils.so.0 -o .libs/libccp4mg-utils.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so.0" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so.0")
libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so")
libtool: link: ( cd ".libs" && rm -f "libccp4mg-utils.la" && ln -s "../libccp4mg-utils.la" "libccp4mg-utils.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
Making all in density-contour
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/density-contour'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o Vectors.lo Vectors.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CIsoSurface.lo CIsoSurface.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o density-contour-triangles.lo density-contour-triangles.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CIsoSurface.cpp  -fPIC -DPIC -o .libs/CIsoSurface.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c density-contour-triangles.cc  -fPIC -DPIC -o .libs/density-contour-triangles.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c Vectors.cpp  -fPIC -DPIC -o .libs/Vectors.o
CIsoSurface.cpp: In instantiation of 'void CIsoSurface<T>::morphVertices() [with T = float]':
CIsoSurface.cpp:1913:16:   required from here
CIsoSurface.cpp:1314:17: warning: unused variable 'offset' [-Wunused-variable]
    unsigned int offset=0;
                 ^
CIsoSurface.cpp:1315:8: warning: unused variable 'n_deleted' [-Wunused-variable]
    int n_deleted = 0;
        ^
CIsoSurface.cpp:1316:8: warning: unused variable 'debug_counter' [-Wunused-variable]
    int debug_counter = 0;
        ^
CIsoSurface.cpp: In instantiation of 'coot::CartesianPairInfo CIsoSurface<T>::returnTriangles(const clipper::Xmap<T>&, const clipper::Coord_frac&, float, coot::Cartesian) const [with T = float]':
CIsoSurface.cpp:1913:16:   required from here
CIsoSurface.cpp:1584:8: warning: unused variable 'face_count_1' [-Wunused-variable]
    int face_count_1 = 0, face_count_2 = 0, face_count_3 = 0;
        ^
CIsoSurface.cpp:1584:26: warning: unused variable 'face_count_2' [-Wunused-variable]
    int face_count_1 = 0, face_count_2 = 0, face_count_3 = 0;
                          ^
CIsoSurface.cpp:1584:44: warning: unused variable 'face_count_3' [-Wunused-variable]
    int face_count_1 = 0, face_count_2 = 0, face_count_3 = 0;
                                            ^
CIsoSurface.cpp:1585:8: warning: unused variable 'not_passed_back_count' [-Wunused-variable]
    int not_passed_back_count = 0;
        ^
CIsoSurface.cpp:1586:14: warning: unused variable 'face' [-Wunused-variable]
    short int face;
              ^
CIsoSurface.cpp: In instantiation of 'void CIsoSurface<T>::check_max_min_vertex_index_from_triangles() [with T = float]':
CIsoSurface.cpp:1913:16:   required from here
CIsoSurface.cpp:1138:17: warning: unused variable 'max_x' [-Wunused-variable]
    unsigned int max_x = -999, max_y = -999, max_z = -999; 
                 ^
CIsoSurface.cpp:1138:31: warning: unused variable 'max_y' [-Wunused-variable]
    unsigned int max_x = -999, max_y = -999, max_z = -999; 
                               ^
CIsoSurface.cpp:1138:45: warning: unused variable 'max_z' [-Wunused-variable]
    unsigned int max_x = -999, max_y = -999, max_z = -999; 
                                             ^
CIsoSurface.cpp:1139:17: warning: unused variable 'min_x' [-Wunused-variable]
    unsigned int min_x =  999, min_y =  999, min_z =  999;
                 ^
CIsoSurface.cpp:1139:31: warning: unused variable 'min_y' [-Wunused-variable]
    unsigned int min_x =  999, min_y =  999, min_z =  999;
                               ^
CIsoSurface.cpp:1139:45: warning: unused variable 'min_z' [-Wunused-variable]
    unsigned int min_x =  999, min_y =  999, min_z =  999;
                                             ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-isosurface.la -rpath /usr/lib Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so.0" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-isosurface.la" && ln -s "../libcoot-isosurface.la" "libcoot-isosurface.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/density-contour'
Making all in db-main
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/db-main'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o db-main.lo db-main.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o db-strands.lo db-strands.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o testdbmain.o testdbmain.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o train-pepflip.o train-pepflip.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c db-main.cc  -fPIC -DPIC -o .libs/db-main.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c db-strands.cc  -fPIC -DPIC -o .libs/db-strands.o
train-pepflip.cc: In function 'int main(int, char**)':
train-pepflip.cc:125:11: warning: unused variable 'frac' [-Wunused-variable]
     float frac = main_chain.mid_oxt_outliers(frag_info.ox_pos, ires+2, cutoff);
           ^
In file included from db-strands.cc:29:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
db-strands.cc: In member function 'std::vector<coot::minimol::molecule> coot::db_strands::get_reference_strands(int, int)':
db-strands.cc:67:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (mv.size() >= n_strands) {
                        ^
db-main.cc: In member function 'void coot::db_main::match_targets_for_pepflip(const coot::minimol::fragment&)':
db-main.cc:932:10: warning: unused variable 'devi' [-Wunused-variable]
    float devi;
          ^
db-main.cc: In member function 'float coot::db_main::mid_oxt_outliers(const clipper::Coord_orth&, int, float)':
db-main.cc:1073:14: warning: variable 'd_sq' set but not used [-Wunused-but-set-variable]
       double d_sq = 0.0;
              ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-db-main.la -rpath /usr/lib db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/db-main.o .libs/db-strands.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so.0" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-db-main.la" && ln -s "../libcoot-db-main.la" "libcoot-db-main.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o testdbmain testdbmain.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o train-pepflip train-pepflip.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/testdbmain testdbmain.o  ./.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/train-pepflip train-pepflip.o  ./.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/db-main'
Making all in ideal
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ideal'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o simple-restraint.lo simple-restraint.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o chirals.lo chirals.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o extra-restraints.lo extra-restraints.cc
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o regularize-minimol.lo regularize-minimol.cc
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libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c chirals.cc  -fPIC -DPIC -o .libs/chirals.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c simple-restraint.cc  -fPIC -DPIC -o .libs/simple-restraint.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c pepflip.cc  -fPIC -DPIC -o .libs/pepflip.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c regularize-minimol.cc  -fPIC -DPIC -o .libs/regularize-minimol.o
In file included from pepflip.cc:23:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
pepflip.cc: In function 'int coot::pepflip(CMMDBManager*, const string&, int, const string&, const string&)':
pepflip.cc:81:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<n_first_residue_atoms; iat++) {
                                ^
pepflip.cc:95:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<n_second_residue_atoms; iat++) {
                                ^
pepflip.cc: In function 'std::vector<clipper::Coord_orth> coot::flip_internal(const std::vector<clipper::Coord_orth>&, const std::vector<CAtom*>&)':
pepflip.cc:184:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0;i<atoms_orth.size(); i++) { 
                                   ^
In file included from simple-restraint.hh:163:0,
                 from regularize-minimol.hh:28,
                 from regularize-minimol.cc:24:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from simple-restraint.hh:163:0,
                 from chirals.cc:32:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from simple-restraint.hh:163:0,
                 from extra-restraints.cc:29:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from simple-restraint.hh:163:0,
                 from simple-restraint.cc:32:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
extra-restraints.cc: In member function 'void coot::restraints_container_t::add_extra_bond_restraints(const coot::extra_restraints_t&)':
extra-restraints.cc:239:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat=0; iat<n_residue_atoms_1; iat++) { 
                                   ^
extra-restraints.cc:249:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat=0; iat<n_residue_atoms_2; iat++) { 
                                   ^
chirals.cc: In function 'std::pair<std::vector<std::basic_string<char> >, std::vector<coot::atom_spec_t> > coot::inverted_chiral_volumes(CMMDBManager*, coot::protein_geometry*, int)':
chirals.cc:181:8: warning: variable 'restraints_status' set but not used [-Wunused-but-set-variable]
    int restraints_status = 1;
        ^
simple-restraint.cc: In member function 'void coot::restraints_container_t::init_from_mol(int, int, short int, short int, short int, const string&, const char*, CMMDBManager*, const std::vector<coot::atom_spec_t>&)':
simple-restraint.cc:282:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_atoms; iat++)
                                    ^
chirals.cc: In member function 'bool coot::restraints_container_t::chiral_hydrogen_needs_pushing(const coot::simple_restraint&, const gsl_vector*) const':
chirals.cc:452:8: warning: unused variable 'n_angles' [-Wunused-variable]
    int n_angles = 0;
        ^
chirals.cc: In member function 'void coot::restraints_container_t::push_chiral_hydrogen(const coot::simple_restraint&, gsl_vector*)':
chirals.cc:597:27: warning: variable 'a' set but not used [-Wunused-but-set-variable]
       clipper::Coord_orth a = a1 - centre;
                           ^
chirals.cc:598:27: warning: variable 'b' set but not used [-Wunused-but-set-variable]
       clipper::Coord_orth b = a2 - centre;
                           ^
chirals.cc:599:27: warning: variable 'c' set but not used [-Wunused-but-set-variable]
       clipper::Coord_orth c = a3 - centre;
                           ^
chirals.cc:576:9: warning: unused variable 'r' [-Wunused-variable]
    bool r = 0;
         ^
simple-restraint.cc: In function 'double coot::distortion_score_rama(const coot::simple_restraint&, const gsl_vector*, const LogRamachandran&)':
simple-restraint.cc:1449:11: warning: unused variable 'distortion' [-Wunused-variable]
    double distortion = 0;
           ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lograma.lo lograma.cpp
simple-restraint.cc: In function 'void coot::my_df_non_bonded(const gsl_vector*, void*, gsl_vector*)':
simple-restraint.cc:2251:16: warning: unused variable 'b_i' [-Wunused-variable]
         double b_i = sqrt(b_i_sqrd);
                ^
simple-restraint.cc: In function 'void coot::my_df_rama(const gsl_vector*, void*, gsl_vector*)':
simple-restraint.cc:2905:16: warning: unused variable 'R' [-Wunused-variable]
         double R = restraints->rama_prob(phir, psir);
                ^
simple-restraint.cc: In member function 'int coot::restraints_container_t::make_restraints(const coot::protein_geometry&, coot::restraint_usage_Flags, short int, float, bool, coot::pseudo_restraint_bond_type)':
simple-restraint.cc:3430:10: warning: unused variable 'n_nbcr' [-Wunused-variable]
      int n_nbcr = make_non_bonded_contact_restraints(bpc, geom);
          ^
simple-restraint.cc: In member function 'void coot::restraints_container_t::mark_OXT(const coot::protein_geometry&)':
simple-restraint.cc:3459:10: warning: unused variable 'res_atom' [-Wunused-variable]
   CAtom *res_atom = NULL;
          ^
simple-restraint.cc: In member function 'std::vector<bool> coot::restraints_container_t::make_non_bonded_fixed_flags(int, int) const':
simple-restraint.cc:3509:9: warning: statement has no effect [-Wunused-value]
   set_0 == 1;
         ^
simple-restraint.cc:3517:9: warning: statement has no effect [-Wunused-value]
   set_1 == 1;
         ^
simple-restraint.cc: In member function 'coot::restraints_container_t::restraint_counts_t coot::restraints_container_t::make_monomer_restraints_by_residue(CResidue*, const coot::protein_geometry&, bool)':
simple-restraint.cc:3967:55: warning: variable 'mod_counts' set but not used [-Wunused-but-set-variable]
      coot::restraints_container_t::restraint_counts_t mod_counts =
                                                       ^
simple-restraint.cc: In member function 'coot::bonded_pair_container_t coot::restraints_container_t::make_link_restraints_from_res_vec(const coot::protein_geometry&, bool)':
simple-restraint.cc:4060:8: warning: unused variable 'iv' [-Wunused-variable]
    int iv = make_link_restraints_by_pairs(geom, bonded_residue_pairs, "Link");
        ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lograma.cpp  -fPIC -DPIC -o .libs/lograma.o
simple-restraint.cc: In member function 'int coot::restraints_container_t::make_link_restraints_by_pairs(const coot::protein_geometry&, const coot::bonded_pair_container_t&, std::string)':
simple-restraint.cc:4076:8: warning: unused variable 'n_link_torsion_restr' [-Wunused-variable]
    int n_link_torsion_restr = 0;
        ^
simple-restraint.cc: In member function 'coot::bonded_pair_container_t coot::restraints_container_t::bonded_residues_from_res_vec(const coot::protein_geometry&) const':
simple-restraint.cc:4386:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int ii=0; ii<residues_vec.size(); ii++) {
                                        ^
simple-restraint.cc:4388:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int jj=ii+1; jj<residues_vec.size(); jj++) {
                                              ^
simple-restraint.cc:4385:8: warning: unused variable 'nres' [-Wunused-variable]
    int nres = residues_vec.size();
        ^
simple-restraint.cc: In member function 'std::string coot::restraints_container_t::general_link_find_close_link_inner(std::vector<std::pair<coot::chem_link, bool> >&, CResidue*, CResidue*, bool, const coot::protein_geometry&) const':
simple-restraint.cc:4833:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int i=0; i<n_residue_atoms; i++) { 
                                 ^
simple-restraint.cc:4840:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int i=0; i<n_residue_atoms; i++) { 
                                 ^
simple-restraint.cc: In member function 'coot::bonded_pair_container_t coot::restraints_container_t::make_flanking_atoms_restraints(const coot::protein_geometry&, bool)':
simple-restraint.cc:4875:8: warning: unused variable 'iv' [-Wunused-variable]
    int iv = make_link_restraints_by_pairs(geom, bonded_residue_pairs, "Flanking residue");
        ^
simple-restraint.cc:4877:8: warning: variable 'n_rama_restraints' set but not used [-Wunused-but-set-variable]
    int n_rama_restraints = -1; // unset, don't output an info line if
        ^
simple-restraint.cc: In member function 'int coot::restraints_container_t::make_non_bonded_contact_restraints(const coot::bonded_pair_container_t&, const coot::protein_geometry&)':
simple-restraint.cc:5222:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_atoms; iat++)
                                    ^
simple-restraint.cc: In member function 'void coot::restraints_container_t::construct_non_bonded_contact_list_by_res_vec(const coot::bonded_pair_container_t&)':
simple-restraint.cc:5441:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<bonded_atom_indices.size(); i++) {
                                             ^
simple-restraint.cc:5442:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<bonded_atom_indices.size(); j++) {
                                                ^
simple-restraint.cc:5472:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_atoms; iat++) {
                                 ^
simple-restraint.cc:5475:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int jat=0; jat<n_atoms; jat++) {
                                ^
simple-restraint.cc: In member function 'void coot::restraints_container_t::mod_plane_add(const coot::chem_mod_plane&, PCResidue)':
simple-restraint.cc:6299:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                    ^
simple-restraint.cc: In member function 'void coot::restraints_container_t::mod_plane_delete(const coot::chem_mod_plane&, PCResidue)':
simple-restraint.cc:6350:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (n_found == it->atom_index.size()) {
                                      ^
simple-restraint.cc:6336:8: warning: unused variable 'in_same_residue' [-Wunused-variable]
   bool in_same_residue = 1;
        ^
simple-restraint.cc: In member function 'int coot::restraints_container_t::get_chiral_hydrogen_index(int, int, int, int) const':
simple-restraint.cc:6370:8: warning: unused variable 'r' [-Wunused-variable]
    int r = -1;
        ^
simple-restraint.cc: In member function 'int coot::restraints_container_t::add_link_angle(std::string, PCResidue, PCResidue, short int, short int, const coot::protein_geometry&)':
simple-restraint.cc:6713:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int ii=0; ii<other_fixed_flags.size(); ii++)
                                               ^
simple-restraint.cc: In member function 'int coot::restraints_container_t::add_link_plane(std::string, PCResidue, PCResidue, short int, short int, const coot::protein_geometry&)':
simple-restraint.cc:7083:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_first_res_atoms; iat++) {
                                 ^
simple-restraint.cc:7091:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_second_res_atoms; iat++) {
                                 ^
simple-restraint.cc:7152:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int indx=0; indx<it->second.size(); indx++) {
                                              ^
simple-restraint.cc:7155:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int ind=0; ind<it->second.size(); ind++) {
                                            ^
simple-restraint.cc:7162:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int ipos=0; ipos<it->second.size(); ipos++)
                                              ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o extra-restraints-kk.lo extra-restraints-kk.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c extra-restraints-kk.cc  -fPIC -DPIC -o .libs/extra-restraints-kk.o
In file included from simple-restraint.hh:163:0,
                 from extra-restraints-kk.cc:26:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
extra-restraints-kk.cc: In member function 'void coot::restraints_container_t::add_extra_start_pos_restraints(const coot::extra_restraints_t&)':
extra-restraints-kk.cc:76:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
          for (unsigned int iat=0; iat<n_residue_atoms_1; iat++) { 
                                       ^
extra-restraints-kk.cc:35:12: warning: variable 'fixed_1' set but not used [-Wunused-but-set-variable]
       bool fixed_1 = 0;
            ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o simple-restraint-kk.lo simple-restraint-kk.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c simple-restraint-kk.cc  -fPIC -DPIC -o .libs/simple-restraint-kk.o
In file included from simple-restraint.hh:163:0,
                 from simple-restraint-kk.cc:26:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
simple-restraint-kk.cc: In function 'void coot::my_df_start_pos(const gsl_vector*, void*, gsl_vector*)':
simple-restraint-kk.cc:89:17: warning: unused variable 'squared_dist' [-Wunused-variable]
          double squared_dist = dist_x * dist_x + dist_y * dist_y + dist_z * dist_z;
                 ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o torsion-bonds.lo torsion-bonds.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c torsion-bonds.cc  -fPIC -DPIC -o .libs/torsion-bonds.o
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o with-geometry.o with-geometry.cc
In file included from simple-restraint.hh:163:0,
                 from torsion-bonds.cc:3:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
torsion-bonds.cc: In function 'std::vector<std::pair<CAtom*, CAtom*> > coot::torsionable_bonds(CMMDBManager*, PPCAtom, int, coot::protein_geometry*)':
torsion-bonds.cc:20:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_selected_atoms; i++) {
                             ^
torsion-bonds.cc: In function 'std::vector<coot::torsion_atom_quad> coot::torsionable_quads(CMMDBManager*, PPCAtom, int, coot::protein_geometry*)':
torsion-bonds.cc:174:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_selected_atoms; i++) { 
                             ^
torsion-bonds.cc: In function 'void coot::multi_residue_torsion_fit_map(CMMDBManager*, const clipper::Xmap<float>&, coot::protein_geometry*)':
torsion-bonds.cc:348:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_selected_atoms; iat++) {
                                    ^
torsion-bonds.cc:388:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iquad=0; iquad<n_quads; iquad++)
                                    ^
torsion-bonds.cc:392:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int itrial=0; itrial<n_trials; itrial++) {
                                      ^
torsion-bonds.cc:396:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iquad=0; iquad<n_quads; iquad++) {
                                       ^
torsion-bonds.cc:413:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int iquad=0; iquad<n_quads; iquad++)
                                          ^
torsion-bonds.cc:377:8: warning: unused variable 'reverse_flag' [-Wunused-variable]
   bool reverse_flag = 1;
        ^
torsion-bonds.cc:391:10: warning: unused variable 'frac' [-Wunused-variable]
   double frac = 360.0/(float) RAND_MAX;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o with-map.o with-map.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from with-geometry.cc:43:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o logramatest.o logramatest.cpp
In file included from simple-restraint.hh:163:0,
                 from with-geometry.cc:45:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from with-map.cc:72:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from simple-restraint.hh:163:0,
                 from with-map.cc:74:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
with-map.cc: In function 'std::vector<std::pair<bool, CResidue*> > fill_residues(const string&, int, int, CMMDBManager*)':
with-map.cc:127:10: warning: unused variable 'at' [-Wunused-variable]
   CAtom *at;
          ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -lgsl -lgslcblas -lm -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -Wl,-z,relro  -o libcoot-ideal.la -rpath /usr/lib simple-restraint.lo chirals.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la -lgsl -lgslcblas -lm -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/simple-restraint.o .libs/chirals.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o .libs/torsion-bonds.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lgsl -lgslcblas -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-ideal.so.0" && ln -s "libcoot-ideal.so.0.0.0" "libcoot-ideal.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-ideal.so" && ln -s "libcoot-ideal.so.0.0.0" "libcoot-ideal.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-ideal.la" && ln -s "../libcoot-ideal.la" "libcoot-ideal.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -lgsl -lgslcblas -lm -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -Wl,-z,relro  -o with-geometry with-geometry.o ./libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../mini-mol/libcoot-mini-mol.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL -I/usr/include   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -DHAVE_GSL  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -lgsl -lgslcblas -lm -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -Wl,-z,relro  -o with-map with-map.o ./libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la ../mini-mol/libcoot-mini-mol.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
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make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ideal'
Making all in ligand
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ligand'
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libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c residue_by_phi_psi.cc  -fPIC -DPIC -o .libs/residue_by_phi_psi.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c ligand.cc  -fPIC -DPIC -o .libs/ligand.o
In file included from ../coot-utils/coot-coord-extras.hh:30:0,
                 from wiggly-ligand.cc:27:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from monomer-utils.cc:23:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
monomer-utils.cc: In member function 'std::vector<coot::atom_index_pair> coot::monomer_utils::get_atom_index_pairs(const std::vector<coot::atom_name_pair>&, PPCAtom, int) const':
monomer-utils.cc:112:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int ipair=0; ipair<atom_name_pairs_in.size(); ipair++) {
                                                    ^
monomer-utils.cc:113:11: warning: unused variable 'ifound' [-Wunused-variable]
       int ifound = 0;
           ^
monomer-utils.cc: In member function 'std::vector<coot::atom_index_quad> coot::monomer_utils::get_atom_index_quads(const std::vector<coot::atom_name_quad>&, PPCAtom, int) const':
monomer-utils.cc:148:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iquad=0; iquad<atom_name_quads_in.size(); iquad++) {
                                                    ^
monomer-utils.cc:149:11: warning: unused variable 'ifound' [-Wunused-variable]
       int ifound = 0;
           ^
monomer-utils.cc:174:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int iquad=0; iquad<atom_name_quads_in.size(); iquad++) {
                                                       ^
residue_by_phi_psi.cc: In member function 'coot::minimol::fragment coot::residue_by_phi_psi::make_2_res_joining_frag(const string&, const coot::phi_psi_pair&, const coot::phi_psi_pair&, int, int, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&) const':
residue_by_phi_psi.cc:337:8: warning: variable 'n_atoms1' set but not used [-Wunused-but-set-variable]
    int n_atoms1, iseqnum1;
        ^
residue_by_phi_psi.cc:337:18: warning: variable 'iseqnum1' set but not used [-Wunused-but-set-variable]
    int n_atoms1, iseqnum1;
                  ^
residue_by_phi_psi.cc:341:8: warning: variable 'n_atoms2' set but not used [-Wunused-but-set-variable]
    int n_atoms2, iseqnum2;
        ^
residue_by_phi_psi.cc:341:18: warning: variable 'iseqnum2' set but not used [-Wunused-but-set-variable]
    int n_atoms2, iseqnum2;
                  ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from residue_by_phi_psi.cc:361:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from wligand.hh:21,
                 from wiggly-ligand.cc:29:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
ligand-extras.cc: In member function 'short int coot::ligand::water_pos_is_chemically_sensible(const clipper::Coord_orth&, const std::vector<clipper::Coord_orth>&) const':
ligand-extras.cc:298:14: warning: unused variable 'min_length' [-Wunused-variable]
       double min_length = 9999.9;
              ^
ligand-extras.cc: In member function 'void coot::ligand::write_waters(const std::vector<clipper::Coord_orth>&, const string&) const':
ligand-extras.cc:314:14: warning: unused variable 'separate_residues' [-Wunused-variable]
    short int separate_residues = 1;
              ^
ligand-extras.cc: In member function 'void coot::ligand::water_fit(float, int)':
ligand-extras.cc:331:14: warning: unused variable 'found_waters_prev_round_flag' [-Wunused-variable]
    short int found_waters_prev_round_flag = 1;
              ^
ligand-extras.cc: In member function 'std::vector<clipper::Coord_orth> coot::ligand::water_fit_internal(float, int)':
ligand-extras.cc:389:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int ic=0; ic<cluster.size(); ic++) {
                                      ^
ligand-extras.cc:435:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int irl=0; irl<iterator_remove_list.size(); irl++)
                                                 ^
ligand-extras.cc: In member function 'void coot::ligand::flood()':
ligand-extras.cc:460:14: warning: variable 'found_waters_prev_round_flag' set but not used [-Wunused-but-set-variable]
    short int found_waters_prev_round_flag = 1;
              ^
ligand-extras.cc: In member function 'coot::minimol::molecule coot::ligand::get_solution(unsigned int, unsigned int) const':
ligand-extras.cc:697:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (iclust < int(final_ligand.size())) {
                                        ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ligand.cc:64:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
wiggly-ligand.cc: In member function 'std::vector<coot::installed_wiggly_ligand_info_t> coot::wligand::install_simple_wiggly_ligands(coot::protein_geometry*, const coot::minimol::molecule&, int, bool, bool)':
wiggly-ligand.cc:198:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    ires<=ligand.fragments[ifrag].max_residue_number();
                                                     ^
wiggly-ligand.cc:53:14: warning: variable 'istat' set but not used [-Wunused-but-set-variable]
    short int istat = 0;
              ^
wiggly-ligand.cc: In member function 'std::pair<float, float> coot::installed_wiggly_ligand_info_t::get_set_and_ideal_torsions(int) const':
wiggly-ligand.cc:753:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i < n_torsions()) {
                          ^
In file included from ligand.cc:66:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
wiggly-ligand.cc: In member function 'std::pair<float, float> coot::installed_wiggly_ligand_info_t::get_set_and_real_torsions(int) const':
wiggly-ligand.cc:775:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i < n_torsions()) {
                          ^
ligand.cc: In member function 'void coot::ligand::find_clusters_internal(float, const std::vector<clipper::Coord_orth>&)':
ligand.cc:860:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int i=0; i<neighb.size(); i++) {
                                              ^
ligand.cc: In member function 'void coot::ligand::cluster_from_point(clipper::Coord_orth, float)':
ligand.cc:989:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<neighb.size(); i++) {
                                            ^
ligand.cc:902:24: warning: variable 'a_cm' set but not used [-Wunused-but-set-variable]
    clipper::Coord_map  a_cm   = a_cf.coord_map(xmap_cluster.grid_sampling());
                        ^
ligand.cc:905:10: warning: unused variable 'br' [-Wunused-variable]
    float br = 3.0;
          ^
ligand.cc: In function 'std::ostream& coot::operator<<(std::ostream&, const coot::ligand_score_card&)':
ligand.cc:1764:8: warning: unused variable 'n_ligand_atoms' [-Wunused-variable]
    int n_ligand_atoms; // non-H.
        ^
ligand.cc:1765:8: warning: unused variable 'ligand_no' [-Wunused-variable]
    int ligand_no;
        ^
ligand.cc:1766:14: warning: unused variable 'many_atoms_fit' [-Wunused-variable]
    short int many_atoms_fit;
              ^
ligand.cc:1767:11: warning: unused variable 'score' [-Wunused-variable]
    double score;
           ^
ligand.cc:1768:11: warning: unused variable 'score_per_atom' [-Wunused-variable]
    double score_per_atom;
           ^
ligand.cc: In member function 'void coot::ligand::score_and_resort_using_correlation(unsigned int, unsigned int)':
ligand.cc:1973:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_ligs; i++) {
                             ^
ligand.cc: In member function 'void coot::ligand::limit_solutions(unsigned int, float, int)':
ligand.cc:2037:17: warning: unused variable 'pre_erase_size' [-Wunused-variable]
    unsigned int pre_erase_size = final_ligand[iclust].size();
                 ^
ligand.cc: In member function 'clipper::Vec3<> coot::ligand::get_rigid_body_angle_components(const std::vector<coot::minimol::atom*>&, const clipper::Coord_orth&, const std::vector<clipper::Grad_orth<float> >&) const':
ligand.cc:2541:11: warning: variable 'sum_alpha' set but not used [-Wunused-but-set-variable]
    double sum_alpha[3];
           ^
ligand.cc:2542:11: warning: variable 'sum_cos_theta' set but not used [-Wunused-but-set-variable]
    double sum_cos_theta[3];
           ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o dunbrack.lo dunbrack.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c dunbrack.cc  -fPIC -DPIC -o .libs/dunbrack.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from rotamer.hh:28,
                 from dunbrack.hh:25,
                 from dunbrack.cc:28:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from chi-angles.hh:27:0,
                 from rotamer.hh:28,
                 from dunbrack.hh:25,
                 from dunbrack.cc:28:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
dunbrack.cc: In member function 'coot::simple_rotamer coot::dunbrack::parse_prl_rotamer_line(const string&, const std::vector<std::basic_string<char> >&)':
dunbrack.cc:356:11: warning: unused variable 'percent_number_parts_index' [-Wunused-variable]
       int percent_number_parts_index = 0; // because we have to also parse percentage out of "<1%c"
           ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o chi-angles-autogen.lo chi-angles-autogen.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c chi-angles-autogen.cc  -fPIC -DPIC -o .libs/chi-angles-autogen.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from chi-angles-autogen.cc:2:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from chi-angles.hh:27:0,
                 from chi-angles-autogen.cc:2:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o chi-angles.lo chi-angles.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c chi-angles.cc  -fPIC -DPIC -o .libs/chi-angles.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o helix-placement.lo helix-placement.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c helix-placement.cc  -fPIC -DPIC -o .libs/helix-placement.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from chi-angles.cc:22:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from chi-angles.hh:27:0,
                 from chi-angles.cc:22:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from helix-placement.hh:24,
                 from helix-placement.cc:43:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
helix-placement.cc: In member function 'clipper::RTop_orth coot::helix_placement::find_best_tube_orientation(clipper::Coord_orth, double, double, float) const':
helix-placement.cc:485:10: warning: unused variable 'anglim' [-Wunused-variable]
    float anglim = alpha1;
          ^
helix-placement.cc: In member function 'clipper::Coord_orth coot::helix_placement::move_helix_centre_point_guess(const clipper::Coord_orth&, float) const':
helix-placement.cc:644:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
    int i=0;
        ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o fast-ss-search.lo fast-ss-search.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c fast-ss-search.cc  -fPIC -DPIC -o .libs/fast-ss-search.o
fast-ss-search.cc: In constructor 'coot::SSfind::Target::Target(coot::SSfind::SSTYPE, int)':
fast-ss-search.cc:78:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(ta2)/sizeof(ta2[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:84:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(ta3)/sizeof(ta3[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:90:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(ta4)/sizeof(ta4[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:96:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(ta3s)/sizeof(ta3s[0]); i++ )  // repr coords
                                                     ^
fast-ss-search.cc:102:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(tb2)/sizeof(tb2[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:108:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(tb3)/sizeof(tb3[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:114:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(tb4)/sizeof(tb4[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:120:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(tb3s)/sizeof(tb3s[0]); i++ )  // repr coords
                                                     ^
fast-ss-search.cc:126:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < sizeof(ta3)/sizeof(ta3[0]); i++ )  // repr coords
                                                   ^
fast-ss-search.cc:155:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int m = 0; m < mp.size(); m++ )
                                ^
fast-ss-search.cc:160:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rep_co.size(); i++ )
                                    ^
fast-ss-search.cc:161:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int m = 0; m < ssops.size(); m++ )
                                     ^
fast-ss-search.cc:167:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int m = 0; m < ssops.size(); m++ )
                                   ^
fast-ss-search.cc: In member function 'void coot::SSfind::prep_xmap(const clipper::Xmap<float>&, double)':
fast-ss-search.cc:184:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < mapbox.size(); i++ ) {
                                    ^
fast-ss-search.cc: In member function 'std::vector<coot::SearchResult> coot::SSfind::search(const std::vector<std::pair<clipper::Coord_orth, clipper::Coord_orth> >&, const std::vector<clipper::RTop_orth>&, double, double) const':
fast-ss-search.cc:224:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < ops.size(); r++ ) {
                                 ^
fast-ss-search.cc:227:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < target_cs.size(); i++ ) {
                                         ^
fast-ss-search.cc:239:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rslts.size(); i++ ) rslts[i].trn = srctrn[i];
                                   ^
fast-ss-search.cc:244:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rslts.size(); i++ ) {  // loop over map
                                   ^
fast-ss-search.cc:251:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int r = 0; r < index_lists.size(); r++ ) {      // loop over rotns
                                             ^
fast-ss-search.cc:260:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ( !( i < index_list.size() ) ) break;
                                ^
fast-ss-search.cc:274:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rslts.size(); i++ )
                                   ^
fast-ss-search.cc: In static member function 'static int coot::fast_secondary_structure_search::join_offset(const std::vector<clipper::Coord_orth>&, const std::vector<clipper::Coord_orth>&)':
fast-ss-search.cc:288:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int a1 = 0; a1 < frag1.size(); a1++ )
                                     ^
fast-ss-search.cc:289:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int a2 = 0; a2 < frag2.size(); a2++ ) {
                                       ^
fast-ss-search.cc: In static member function 'static double coot::fast_secondary_structure_search::join_score(const std::vector<clipper::Coord_orth>&, const std::vector<clipper::Coord_orth>&)':
fast-ss-search.cc:305:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int a1 = 0; a1 < frag1.size(); a1++ ) {
                                     ^
fast-ss-search.cc:307:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( a2 >= 0 && a2 < frag2.size() ) {
                                     ^
fast-ss-search.cc: In static member function 'static std::vector<std::vector<clipper::Coord_orth> > coot::fast_secondary_structure_search::join(std::vector<std::vector<clipper::Coord_orth> >, int)':
fast-ss-search.cc:320:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int f = 0; f < frags.size(); f++ ) if ( frags[f].size() < 4 ) extn = 0;
                                   ^
fast-ss-search.cc:323:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f = 0; f < frags.size(); f++ ) {
                                     ^
fast-ss-search.cc:343:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int f = 0; f < wghts.size(); f++ ) {
                                   ^
fast-ss-search.cc:347:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int a = 0; a < wghts[f].size(); a++ )
                                        ^
fast-ss-search.cc:353:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int f1 = 0; f1 < frags.size(); f1++ )
                                     ^
fast-ss-search.cc:354:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f2 = f1+1; f2 < frags.size(); f2++ )
                                          ^
fast-ss-search.cc:358:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < frags.size()*frags.size(); i++ ) {
                                                ^
fast-ss-search.cc:362:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f1 = 0; f1 < frags.size(); f1++ )
                                       ^
fast-ss-search.cc:363:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int f2 = f1+1; f2 < frags.size(); f2++ )
                                            ^
fast-ss-search.cc:376:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if ( a1 >= 0 && a1 < frags[j1].size() ) {
                                           ^
fast-ss-search.cc:380:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if ( a2 >= 0 && a2 < frags[j2].size() ) {
                                           ^
fast-ss-search.cc:390:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f2 = j1+1; f2 < frags.size(); f2++ )
                                          ^
fast-ss-search.cc:392:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f2 = j2+1; f2 < frags.size(); f2++ )
                                          ^
fast-ss-search.cc:398:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int f = 0; f < frags.size(); f++ )
                                   ^
fast-ss-search.cc:399:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( frags[f].size() > 2*extn ) {
                              ^
fast-ss-search.cc:401:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int a = 0; a < fr.size(); a++ ) fr[a] = frags[f][a+extn];
                                    ^
fast-ss-search.cc: In member function 'void coot::fast_secondary_structure_search::operator()(const clipper::Xmap<float>&, const clipper::Coord_orth&, double, std::vector<coot::SSfind::Target>)':
fast-ss-search.cc:444:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int t = 0; t < targets.size(); t++ ) {
                                     ^
fast-ss-search.cc:446:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < target_cs.size(); i++ ) {
                                         ^
fast-ss-search.cc:467:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int t = 0; t < targets.size(); t++ ) {
                                     ^
fast-ss-search.cc:476:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < rslts.size(); i++ )
                                     ^
fast-ss-search.cc:485:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < rsltf.size(); i++ ) {
                                     ^
fast-ss-search.cc:495:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < rtops.size(); i++ ) {
                                     ^
fast-ss-search.cc:515:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < rtops.size(); i++ ) {
                                     ^
fast-ss-search.cc:516:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int r = 0; r < ss.size(); r++ )
                                    ^
fast-ss-search.cc:525:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < ssj.size(); i++ ) sscoord.push_back( ssj[i] );
                                   ^
fast-ss-search.cc:544:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int c = 0; c < sscoord.size(); c++ ) {
                                     ^
fast-ss-search.cc:548:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( c1 >= 0 && c1 < cnames.length() ) cname += cnames.substr(c1,1);
                                        ^
fast-ss-search.cc:549:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( c2 >= 0 && c2 < cnames.length() ) cname += cnames.substr(c2,1);
                                        ^
fast-ss-search.cc:551:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int r = 0; r < sscoord[c].size(); r++ ) {
                                          ^
fast-ss-search.cc:411:53: warning: typedef 'MRI' locally defined but not used [-Wunused-local-typedefs]
   typedef clipper::Xmap<float>::Map_reference_index MRI;
                                                     ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rigid-body.lo rigid-body.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c rigid-body.cc  -fPIC -DPIC -o .libs/rigid-body.o
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from rigid-body.cc:26:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
rigid-body.cc: In function 'void coot::rigid_body_fit(coot::minimol::molecule*, const clipper::Xmap<float>&)':
rigid-body.cc:52:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        ires<(*m)[ifrag].max_residue_number(); ires++) {
                                            ^
rigid-body.cc:67:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<atoms.size(); i++) {
                              ^
rigid-body.cc:86:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int ii=0; ii<atoms.size(); ii++) {
                                ^
rigid-body.cc:130:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    ires<=(*m)[ifrag].max_residue_number();
                                         ^
rigid-body.cc: In function 'clipper::Vec3<> coot::get_rigid_body_angle_components(const std::vector<coot::minimol::atom*>&, const clipper::Coord_orth&, const std::vector<clipper::Grad_orth<float> >&, double)':
rigid-body.cc:182:11: warning: variable 'sum_alpha' set but not used [-Wunused-but-set-variable]
    double sum_alpha[3];
           ^
rigid-body.cc:183:11: warning: variable 'sum_cos_theta' set but not used [-Wunused-but-set-variable]
    double sum_cos_theta[3];
           ^
rigid-body.cc: In function 'float coot::score_molecule(const coot::minimol::molecule&, const clipper::Xmap<float>&)':
rigid-body.cc:277:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int ires=m[ifrag].min_res_no(); ires<m[ifrag].max_residue_number();
                                                                                      ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o ideal-rna.lo ideal-rna.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c ideal-rna.cc  -fPIC -DPIC -o .libs/ideal-rna.o
In file included from ideal-rna.cc:24:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
ideal-rna.cc: In member function 'CMMDBManager* coot::ideal_rna::make_molecule()':
ideal-rna.cc:93:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int iseq=0; iseq<seq.length(); iseq++) {
                                       ^
ideal-rna.cc:124:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int iseq=0; iseq<seq.length(); iseq++) {
                                   ^
ideal-rna.cc: In member function 'void coot::ideal_rna::fix_up_residue_and_atom_names(CResidue*, bool)':
ideal-rna.cc:176:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                 ^
ideal-rna.cc:194:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o richardson-rotamers.lo richardson-rotamers.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c richardson-rotamers.cc  -fPIC -DPIC -o .libs/richardson-rotamers.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o richardson-rotamer.lo richardson-rotamer.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c richardson-rotamer.cc  -fPIC -DPIC -o .libs/richardson-rotamer.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rotamer.lo rotamer.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c rotamer.cc  -fPIC -DPIC -o .libs/rotamer.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from richardson-rotamers.cc:1:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from chi-angles.hh:27:0,
                 from richardson-rotamers.cc:1:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from rotamer.hh:28,
                 from richardson-rotamer.hh:25,
                 from richardson-rotamer.cc:2:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o torsion-general.lo torsion-general.cc
In file included from chi-angles.hh:27:0,
                 from rotamer.hh:28,
                 from richardson-rotamer.hh:25,
                 from richardson-rotamer.cc:2:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from rotamer.hh:28,
                 from rotamer.cc:28:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c torsion-general.cc  -fPIC -DPIC -o .libs/torsion-general.o
In file included from chi-angles.hh:27:0,
                 from rotamer.hh:28,
                 from rotamer.cc:28:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
rotamer.cc: In member function 'coot::rotamer_probability_info_t coot::rotamer::probability_of_this_rotamer()':
rotamer.cc:232:14: warning: variable 'state' set but not used [-Wunused-but-set-variable]
    short int state;  // flag for assigned,                    1 
              ^
rotamer.cc: In member function 'CResidue* coot::rotamer::GetResidue(const coot::dictionary_residue_restraints_t&, int) const':
rotamer.cc:604:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        (i_rot >= rots.size())) { 
                            ^
rotamer.cc: In member function 'CResidue* coot::rotamer::GetResidue_old(int) const':
rotamer.cc:696:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        (i_rot >= rots.size())) { 
                            ^
rotamer.cc:799:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int i=0; i<coords.size(); i++)
                                 ^
rotamer.cc:806:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int ic=0; ic<contact_indices.size(); ic++) {
                                             ^
rotamer.cc:807:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int jc=0; jc<contact_indices[ic].size(); jc++) {
                                                    ^
rotamer.cc:831:16: warning: variable 'ctors' set but not used [-Wunused-but-set-variable]
         double ctors = tree.GetCoord(atom_index_pairs[ibond].index2)->GetChild(0)->GetParentDihedralAngle();
                ^
rotamer.cc: In member function 'std::vector<CAtom*> coot::rotamer::ordered_residue_atoms(CResidue*) const':
rotamer.cc:1077:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int ian=0; ian<atom_order.size(); ian++) {
                                          ^
rotamer.cc:1078:19: warning: variable 'marked_atom' set but not used [-Wunused-but-set-variable]
         short int marked_atom = 0;
                   ^
rotamer.cc:1090:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int in_atom=0; in_atom<atom_vec.size(); in_atom++) {
                                                   ^
rotamer.cc:1100:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<other_atoms.size(); i++)
                                       ^
rotamer.cc: In member function 'std::vector<coot::simple_rotamer> coot::rotamer::rotamers(const string&, float) const':
rotamer.cc:1117:14: warning: variable 'found_res' set but not used [-Wunused-but-set-variable]
    short int found_res = 0;
              ^
In file included from torsion-general.hh:25:0,
                 from torsion-general.cc:23:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
torsion-general.cc: In member function 'int coot::torsion_general::change_by(double, Tree*)':
torsion-general.cc:112:15: warning: unused variable 'tvc0' [-Wunused-variable]
   TreeVertex *tvc0 = tv->GetChild(0);
               ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rotamer-tables.lo rotamer-tables.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c rotamer-tables.cc  -fPIC -DPIC -o .libs/rotamer-tables.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from rotamer.hh:28,
                 from rotamer-tables.cc:27:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from chi-angles.hh:27:0,
                 from rotamer.hh:28,
                 from rotamer-tables.cc:27:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
rotamer-tables.cc: In member function 'void coot::a_rotamer_table::fill_chi_1(const string&)':
rotamer-tables.cc:71:8: warning: unused variable 'chi_count' [-Wunused-variable]
    int chi_count = 0;
        ^
rotamer-tables.cc: In member function 'void coot::a_rotamer_table::fill_chi_1_2(const string&)':
rotamer-tables.cc:129:8: warning: unused variable 'chi_count' [-Wunused-variable]
    int chi_count = 0;
        ^
rotamer-tables.cc:132:13: warning: unused variable 'n_x3_obj_count' [-Wunused-variable]
    long int n_x3_obj_count = -1;
             ^
rotamer-tables.cc:133:13: warning: unused variable 'n_x4_obj_count' [-Wunused-variable]
    long int n_x4_obj_count = -1;
             ^
rotamer-tables.cc: In member function 'void coot::a_rotamer_table::fill_chi_1_2_3(const string&)':
rotamer-tables.cc:226:8: warning: unused variable 'chi_count' [-Wunused-variable]
    int chi_count = 0;
        ^
rotamer-tables.cc: In member function 'void coot::a_rotamer_table::fill_chi_1_2_3_4(const string&)':
rotamer-tables.cc:335:8: warning: unused variable 'chi_count' [-Wunused-variable]
    int chi_count = 0;
        ^
rotamer-tables.cc: In member function 'coot::rotamer_probability_info_t coot::rotamer_probability_tables::probability_this_rotamer(unsigned int, const std::vector<std::pair<int, float> >&) const':
rotamer-tables.cc:509:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (bins.size() != n) {
                       ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o primitive-chi-angles.lo primitive-chi-angles.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c primitive-chi-angles.cc  -fPIC -DPIC -o .libs/primitive-chi-angles.o
In file included from primitive-chi-angles.cc:6:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
primitive-chi-angles.cc: In member function 'std::vector<coot::atom_index_quad> coot::primitive_chi_angles::get_atom_index_quads(const std::vector<coot::atom_name_quad>&, PPCAtom, int) const':
primitive-chi-angles.cc:245:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int iquad=0; iquad<atom_name_quads_in.size(); iquad++) {
                                                    ^
primitive-chi-angles.cc:246:11: warning: unused variable 'ifound' [-Wunused-variable]
       int ifound = 0;
           ^
primitive-chi-angles.cc:271:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int iquad=0; iquad<atom_name_quads_in.size(); iquad++) {
                                                       ^
primitive-chi-angles.cc: In member function 'std::vector<coot::alt_confed_atom_index_quad> coot::primitive_chi_angles::get_quads_using_altconfs(const std::vector<coot::atom_name_quad>&, CResidue*) const':
primitive-chi-angles.cc:325:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int iquad=0; iquad<atom_name_quads.size(); iquad++) {
                                                    ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o dipole.lo dipole.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c dipole.cc  -fPIC -DPIC -o .libs/dipole.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from dipole.cc:23:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
dipole.cc: In member function 'void coot::dipole::init(std::vector<std::pair<coot::dictionary_residue_restraints_t, CResidue*> >)':
dipole.cc:115:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int ii=0; ii<charged_points.size(); ii++) { 
                                          ^
dipole.cc: In member function 'std::vector<std::pair<CAtom*, float> > coot::dipole::charged_atoms(CResidue*, const coot::dictionary_residue_restraints_t&) const':
dipole.cc:165:12: warning: unused variable 'found_match' [-Wunused-variable]
       bool found_match = 0;
            ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o base-pairing.lo base-pairing.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c base-pairing.cc  -fPIC -DPIC -o .libs/base-pairing.o
In file included from base-pairing.cc:23:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
base-pairing.cc: In function 'std::pair<bool, clipper::RTop_orth> coot::base_pair_match_matix(CResidue*, CResidue*)':
base-pairing.cc:234:11: warning: unused variable 'found_atoms' [-Wunused-variable]
       int found_atoms = 0;
           ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o backrub-rotamer.lo backrub-rotamer.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c backrub-rotamer.cc  -fPIC -DPIC -o .libs/backrub-rotamer.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from chi-angles.hh:25,
                 from rotamer.hh:28,
                 from richardson-rotamer.hh:25,
                 from backrub-rotamer.cc:27:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o find-ligand.o find-ligand.cc
In file included from chi-angles.hh:27:0,
                 from rotamer.hh:28,
                 from richardson-rotamer.hh:25,
                 from backrub-rotamer.cc:27:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
backrub-rotamer.cc: In member function 'std::pair<coot::minimol::molecule, float> coot::backrub::search(const coot::dictionary_residue_restraints_t&)':
backrub-rotamer.cc:64:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int irot=0; irot<n_rotatmers; irot++) {
                                   ^
backrub-rotamer.cc: In member function 'coot::minimol::fragment coot::backrub::make_test_fragment(CResidue*, double) const':
backrub-rotamer.cc:164:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ires=f.min_res_no(); ires<=f.max_residue_number(); ires++) {
                                                                      ^
backrub-rotamer.cc:165:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<f[ires].n_atoms(); iat++) {
                                                    ^
backrub-rotamer.cc: In member function 'float coot::backrub::residue_radius(const clipper::Coord_orth&)':
backrub-rotamer.cc:220:10: warning: unused variable 'sum_x' [-Wunused-variable]
    float sum_x=0, sum_y=0, sum_z=0;
          ^
backrub-rotamer.cc:220:19: warning: unused variable 'sum_y' [-Wunused-variable]
    float sum_x=0, sum_y=0, sum_z=0;
                   ^
backrub-rotamer.cc:220:28: warning: unused variable 'sum_z' [-Wunused-variable]
    float sum_x=0, sum_y=0, sum_z=0;
                            ^
backrub-rotamer.cc: In member function 'float coot::backrub::score_fragment(coot::minimol::fragment&) const':
backrub-rotamer.cc:242:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ires=frag.min_res_no(); ires<=frag.max_residue_number(); ires++) {
                                                                            ^
backrub-rotamer.cc:243:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<frag[ires].n_atoms(); iat++) {
                                                       ^
backrub-rotamer.cc: In member function 'double coot::backrub::sample_individual_peptide(CResidue*, double, coot::minimol::fragment*, CResidue*, CResidue*, bool) const':
backrub-rotamer.cc:448:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        ires<=(f->max_residue_number()+1-res_offset);
                                                   ^
backrub-rotamer.cc:450:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat=0; iat<(*f)[ires].n_atoms(); iat++) {
                                                      ^
backrub-rotamer.cc:451:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ires == resno_for_CO) {
                     ^
backrub-rotamer.cc:432:11: warning: variable 'resno_for_N' set but not used [-Wunused-but-set-variable]
       int resno_for_N  = next_resno;
           ^
backrub-rotamer.cc: In member function 'void coot::backrub::apply_back_rotation(coot::minimol::fragment*, bool, double) const':
backrub-rotamer.cc:527:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  ires<=(f->max_residue_number()+1-res_offset);
                                             ^
backrub-rotamer.cc:529:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<(*f)[ires].n_atoms(); iat++) {
                                                       ^
backrub-rotamer.cc:531:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (ires == resno_for_CO) {
               ^
backrub-rotamer.cc:537:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (ires == resno_for_N) {
               ^
backrub-rotamer.cc: In member function 'float coot::backrub::get_clash_score(const coot::minimol::molecule&, PPCAtom, int) const':
backrub-rotamer.cc:688:9: warning: statement has no effect [-Wunused-value]
    dlsq == 0.001; 
         ^
backrub-rotamer.cc:659:11: warning: unused variable 'max_dev_residue_pos' [-Wunused-variable]
    double max_dev_residue_pos = rotamer_info.first;
           ^
backrub-rotamer.cc:660:24: warning: variable 'mean_residue_pos' set but not used [-Wunused-but-set-variable]
    clipper::Coord_orth mean_residue_pos = rotamer_info.second;
                        ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from monomer-utils.hh:33,
                 from wligand.hh:21,
                 from find-ligand.cc:46:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
find-ligand.cc: In function 'int main(int, char**)':
find-ligand.cc:315:10: warning: unused variable 'n_cluster' [-Wunused-variable]
      int n_cluster = atoi(n_cluster_string.c_str());
          ^
find-ligand.cc:94:13: warning: unused variable 'absolute_level' [-Wunused-variable]
       float absolute_level = 0.0;
             ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o find-waters.o find-waters.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from find-waters.cc:42:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from find-waters.cc:44:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
find-waters.cc: In function 'int main(int, char**)':
find-waters.cc:199:17: warning: variable 'do_it_with_map' set but not used [-Wunused-but-set-variable]
       short int do_it_with_map = 0;
                 ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-ligand.la -rpath /usr/lib ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/coords/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so -lgsl -lgslcblas ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -fopenmp -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o findligand-real find-ligand.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o findwaters-real find-waters.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
libtool: link: g++ -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/findwaters-real find-waters.o  ./.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.7/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs/libccp4mg-utils.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../db-main/.libs/libcoot-db-main.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lm -fopenmp
libtool: link: g++ -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/findligand-real find-ligand.o  ./.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.7/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs/libccp4mg-utils.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lm -fopenmp
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ligand'
Making all in high-res
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/high-res'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o high-res.lo high-res.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-atom-graph.lo coot-atom-graph.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o residue-distortions.lo residue-distortions.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o sequence-assignment.lo sequence-assignment.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c high-res.cc  -fPIC -DPIC -o .libs/high-res.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c coot-atom-graph.cc  -fPIC -DPIC -o .libs/coot-atom-graph.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c residue-distortions.cc  -fPIC -DPIC -o .libs/residue-distortions.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c sequence-assignment.cc  -fPIC -DPIC -o .libs/sequence-assignment.o
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from high-res.cc:24:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from sequence-assignment.cc:31:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
residue-distortions.cc: In member function 'void coot::atom_graph::score_all_side_chain_types(int, const std::vector<coot::node_info>&, coot::sequence_assignment::side_chain_score_t*) const':
residue-distortions.cc:46:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<sc_nodes.size(); i++) {
                                     ^
residue-distortions.cc: In member function 'double coot::atom_graph::distortion_score_side_chain_old(int, const string&, const std::vector<coot::node_info>&) const':
residue-distortions.cc:90:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<sc_nodes.size(); i++) {
                                     ^
residue-distortions.cc: In member function 'double coot::atom_graph::distortion_score_pro(const std::vector<clipper::Coord_orth>&) const':
residue-distortions.cc:515:14: warning: unused variable 'len6' [-Wunused-variable]
       double len6 = clipper::Coord_orth::length(c[1], c[3]); // CB  CD  angle
              ^
residue-distortions.cc: In member function 'double coot::atom_graph::distortion_score_phe(const std::vector<clipper::Coord_orth>&) const':
residue-distortions.cc:541:14: warning: unused variable 'len6' [-Wunused-variable]
       double len6 = clipper::Coord_orth::length(c[4], c[6]); //   bond
              ^
residue-distortions.cc:542:14: warning: unused variable 'len7' [-Wunused-variable]
       double len7 = clipper::Coord_orth::length(c[5], c[7]); //   bond
              ^
residue-distortions.cc:543:14: warning: unused variable 'len8' [-Wunused-variable]
       double len8 = clipper::Coord_orth::length(c[6], c[7]); //   bond
              ^
residue-distortions.cc:545:14: warning: unused variable 'len9' [-Wunused-variable]
       double len9 =  clipper::Coord_orth::length(c[0], c[2]); // 
              ^
residue-distortions.cc:546:14: warning: unused variable 'len10' [-Wunused-variable]
       double len10 = clipper::Coord_orth::length(c[1], c[4]); // 
              ^
residue-distortions.cc:547:14: warning: unused variable 'len11' [-Wunused-variable]
       double len11 = clipper::Coord_orth::length(c[1], c[3]); // 
              ^
residue-distortions.cc:548:14: warning: unused variable 'len12' [-Wunused-variable]
       double len12 = clipper::Coord_orth::length(c[2], c[6]); // 
              ^
residue-distortions.cc:549:14: warning: unused variable 'len13' [-Wunused-variable]
       double len13 = clipper::Coord_orth::length(c[2], c[5]); // 
              ^
residue-distortions.cc:550:14: warning: unused variable 'len14' [-Wunused-variable]
       double len14 = clipper::Coord_orth::length(c[6], c[5]); //
              ^
residue-distortions.cc:552:14: warning: unused variable 'torsion1' [-Wunused-variable]
       double torsion1 = clipper::Coord_orth::torsion(c[2],c[4],c[6],c[7]);
              ^
residue-distortions.cc:553:14: warning: unused variable 'torsion2' [-Wunused-variable]
       double torsion2 = clipper::Coord_orth::torsion(c[2],c[3],c[5],c[7]);
              ^
residue-distortions.cc:555:14: warning: unused variable 'abs_cv1' [-Wunused-variable]
       double abs_cv1 = abs_chiral_vol(c[2], c[1], c[3], c[4]);
              ^
residue-distortions.cc: In member function 'double coot::atom_graph::distortion_score_tyr(const std::vector<clipper::Coord_orth>&) const':
residue-distortions.cc:579:14: warning: unused variable 'len6' [-Wunused-variable]
       double len6 = clipper::Coord_orth::length(c[4], c[6]); //   bond
              ^
residue-distortions.cc:580:14: warning: unused variable 'len7' [-Wunused-variable]
       double len7 = clipper::Coord_orth::length(c[5], c[7]); //   bond
              ^
residue-distortions.cc:581:14: warning: unused variable 'len8' [-Wunused-variable]
       double len8 = clipper::Coord_orth::length(c[6], c[7]); //   bond
              ^
residue-distortions.cc:583:14: warning: unused variable 'len9' [-Wunused-variable]
       double len9 =  clipper::Coord_orth::length(c[0], c[2]); // 
              ^
residue-distortions.cc:584:14: warning: unused variable 'len10' [-Wunused-variable]
       double len10 = clipper::Coord_orth::length(c[1], c[4]); // 
              ^
residue-distortions.cc:585:14: warning: unused variable 'len11' [-Wunused-variable]
       double len11 = clipper::Coord_orth::length(c[1], c[3]); // 
              ^
residue-distortions.cc:586:14: warning: unused variable 'len12' [-Wunused-variable]
       double len12 = clipper::Coord_orth::length(c[2], c[6]); // 
              ^
residue-distortions.cc:587:14: warning: unused variable 'len13' [-Wunused-variable]
       double len13 = clipper::Coord_orth::length(c[2], c[5]); // 
              ^
residue-distortions.cc:588:14: warning: unused variable 'len14' [-Wunused-variable]
       double len14 = clipper::Coord_orth::length(c[6], c[5]); //
              ^
residue-distortions.cc:590:14: warning: unused variable 'torsion1' [-Wunused-variable]
       double torsion1 = clipper::Coord_orth::torsion(c[2],c[4],c[6],c[7]);
              ^
residue-distortions.cc:591:14: warning: unused variable 'torsion2' [-Wunused-variable]
       double torsion2 = clipper::Coord_orth::torsion(c[2],c[3],c[5],c[7]);
              ^
residue-distortions.cc:593:14: warning: unused variable 'abs_cv1' [-Wunused-variable]
       double abs_cv1 = abs_chiral_vol(c[2], c[1], c[3], c[4]);
              ^
coot-atom-graph.cc: In constructor 'coot::atom_graph::atom_graph(CMMDBManager*, const std::vector<std::vector<coot::node_info> >&, const std::vector<clipper::Coord_orth>&)':
coot-atom-graph.cc:47:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int iat=0; iat<coords.size(); iat++)
                                       ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::sort()':
coot-atom-graph.cc:117:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int itip=0; itip<tips.size(); itip++) {
                                    ^
coot-atom-graph.cc:159:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int iat=0; iat<atom_info.size(); iat++) {
                                      ^
coot-atom-graph.cc:160:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<atom_info[iat].size(); j++) { 
                                           ^
coot-atom-graph.cc:174:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int itip=0; itip<tips.size(); itip++)
                                    ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::trace_along(int, int)':
coot-atom-graph.cc:194:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<nodes[ic].size(); i++) {
                                   ^
coot-atom-graph.cc: In member function 'std::vector<std::vector<coot::node_info> > coot::atom_graph::get_trace(int) const':
coot-atom-graph.cc:238:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<con_local.size(); i++) 
                                   ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::digraph_trace_along(int, int, std::vector<std::vector<coot::node_info> >*, std::vector<int>*) const':
coot-atom-graph.cc:261:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<nodes[inode].size(); i++) {
                                      ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::assign_c_betas()':
coot-atom-graph.cc:274:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int index=0; index<atoms.size(); index++) {
                                       ^
coot-atom-graph.cc:278:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j<nodes[index].size(); j++) {
                                        ^
coot-atom-graph.cc: In member function 'short int coot::atom_graph::is_c_alpha_p(int) const':
coot-atom-graph.cc:311:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (index < atoms.size() && index >= 0) { 
                           ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::assign_waters()':
coot-atom-graph.cc:327:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<nodes.size(); i++) {
                               ^
coot-atom-graph.cc: In member function 'coot::chain_helper_info coot::atom_graph::peptide_search(const std::vector<std::vector<coot::node_info> >&, int, const coot::chain_helper_info&, short int)':
coot-atom-graph.cc:403:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int ip1 = 0; ip1<t[i_node_peptide_start].size(); ip1++) {
                                                          ^
coot-atom-graph.cc:407:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int ip2 = 0; ip2<t[t_index_2].size(); ip2++) {
                                           ^
coot-atom-graph.cc:411:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int ip3 = 0; ip3<t[t_index_3].size(); ip3++) {
                                              ^
coot-atom-graph.cc:426:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int ip4=0; ip4<t[t_index_4].size(); ip4++) { 
                                           ^
coot-atom-graph.cc:429:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int ip5=0; ip5<t[t_index_5].size(); ip5++) { 
                                              ^
coot-atom-graph.cc:432:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int ip6=0; ip6<t[t_index_6].size(); ip6++) { 
                                          ^
coot-atom-graph.cc:424:31: warning: variable 't_index_7' set but not used [-Wunused-but-set-variable]
     int t_index_5, t_index_6, t_index_7;
                               ^
coot-atom-graph.cc:356:8: warning: variable 'dir_offset' set but not used [-Wunused-but-set-variable]
    int dir_offset = 0;
        ^
coot-atom-graph.cc:360:8: warning: unused variable 'skip' [-Wunused-variable]
    int skip = 0;
        ^
coot-atom-graph.cc:381:8: warning: unused variable 'i_node_peptide_start' [-Wunused-variable]
    int i_node_peptide_start = i_node_start;
        ^
coot-atom-graph.cc: In member function 'double coot::atom_graph::peptide_distortion_score(short int, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&) const':
coot-atom-graph.cc:918:14: warning: unused variable 'len4' [-Wunused-variable]
       double len4 = clipper::Coord_orth::length(a1, a4);
              ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::write_molecule_from_atom_info(const string&) const':
coot-atom-graph.cc:952:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<atom_info.size(); i++) {
                                   ^
coot-atom-graph.cc:959:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<atom_info.size(); i++) {
                                   ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from ../ligand/dunbrack.hh:25,
                 from sequence-assignment.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
coot-atom-graph.cc:976:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j<atom_info[i].size(); j++) {
                                     ^
coot-atom-graph.cc:949:8: warning: unused variable 'fragment_no' [-Wunused-variable]
    int fragment_no;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
coot-atom-graph.cc: In member function 'void coot::atom_graph::sidechains_search()':
coot-atom-graph.cc:1048:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<atom_info.size(); i++) { 
                                   ^
coot-atom-graph.cc:1049:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<atom_info[i].size(); j++) { 
                                         ^
coot-atom-graph.cc:1032:11: warning: unused variable 'd' [-Wunused-variable]
    double d;
           ^
coot-atom-graph.cc:1033:8: warning: unused variable 'i_node_ca' [-Wunused-variable]
    int i_node_ca; 
        ^
coot-atom-graph.cc: In member function 'std::vector<coot::node_info> coot::atom_graph::get_side_chain_nodes(int, coot::sequence_assignment::side_chain_name_index) const':
coot-atom-graph.cc:1088:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j<nodes[i_node_ca].size(); j++) {
                                         ^
coot-atom-graph.cc:1095:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int ati=0; ati<nodes[i_node_ca].size(); ati++) {
                                                ^
In file included from high-res.cc:27:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
high-res.cc: In constructor 'coot::high_res::high_res(const coot::minimol::molecule&)':
high-res.cc:40:24: warning: variable 'target_pos' set but not used [-Wunused-but-set-variable]
    clipper::Coord_orth target_pos = middle_pos.first;
                        ^
high-res.cc: In member function 'void coot::high_res::fill_globular_protein(const coot::minimol::molecule&, const clipper::Coord_orth&, CMMDBManager*)':
high-res.cc:147:11: warning: variable 'one_over_n_atoms' set but not used [-Wunused-but-set-variable]
    double one_over_n_atoms; 
           ^
sequence-assignment.cc: In member function 'int coot::sequence_assignment::scored_chain_info_t::outstanding_slider_position(const std::vector<float>&) const':
sequence-assignment.cc:383:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (i != best_val_idx) { 
            ^
sequence-assignment.cc: In member function 'short int coot::sequence_assignment::side_chain_score_t::cache_standard_residues()':
sequence-assignment.cc:652:14: warning: unused variable 'res' [-Wunused-variable]
    CResidue *res;
              ^
sequence-assignment.cc: In member function 'std::vector<coot::residue_range_t> coot::sequence_assignment::side_chain_score_t::find_unassigned_regions(float)':
sequence-assignment.cc:712:16: warning: unused variable 'stop_residue' [-Wunused-variable]
      PCResidue stop_residue;
                ^
sequence-assignment.cc:714:10: warning: unused variable 'consecutive_ala_count' [-Wunused-variable]
      int consecutive_ala_count = 0;
          ^
sequence-assignment.cc: In member function 'std::vector<coot::sequence_assignment::sequence_range_t> coot::sequence_assignment::side_chain_score_t::find_unassigned_sequence(const coot::residue_range_t&) const':
sequence-assignment.cc:888:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (sequence_infos[is].residue_info.size() > required_range_size) {
                                                    ^
sequence-assignment.cc: In member function 'void coot::sequence_assignment::side_chain_score_t::test_residue_range_marking()':
sequence-assignment.cc:951:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=start_ass; i<end_ass && i<sequence_infos[0].residue_info.size(); i++) {
                                     ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/ideal/.libs -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/db-main/.libs -L/builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.7/coords/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.7/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so -lgsl -lgslcblas /builddir/build/BUILD/coot-0.7/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs/libccp4mg-utils.so -lpng /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so.0" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/high-res'
Making all in build
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/build'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o CalphaBuild.lo CalphaBuild.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o testcabuild.o testcabuild.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c CalphaBuild.cc  -fPIC -DPIC -o .libs/CalphaBuild.o
CalphaBuild.cc: In member function 'std::vector<coot::scored_skel_coord> coot::CalphaBuild::next_ca_by_skel(const std::vector<clipper::Coord_orth>&, const clipper::Coord_grid&, short int, float, const clipper::Xmap<int>&, const clipper::Xmap<float>&, float, const clipper::Xmap<coot::SkeletonTreeNode>&) const':
CalphaBuild.cc:67:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<scored_positions.size(); i++) { 
                                          ^
CalphaBuild.cc: In member function 'std::vector<coot::scored_skel_coord> coot::CalphaBuild::next_ca_internal(const std::vector<clipper::Coord_orth>&, const clipper::Coord_grid&, short int, float, const clipper::Xmap<int>&, const clipper::Xmap<float>&, float, const clipper::Xmap<coot::SkeletonTreeNode>&, int) const':
CalphaBuild.cc:198:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i=0; i<ssc.size(); i++) {
                               ^
CalphaBuild.cc:237:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i=0; i<ssc.size(); i++) {
                               ^
CalphaBuild.cc:115:10: warning: unused variable 'skel_dist_lim_max' [-Wunused-variable]
    float skel_dist_lim_max = 4.3; // A
          ^
CalphaBuild.cc:116:10: warning: unused variable 'skel_dist_lim_min' [-Wunused-variable]
    float skel_dist_lim_min = 2.5; // A la Oldfield 2003.
          ^
CalphaBuild.cc: In member function 'std::vector<coot::scored_skel_coord> coot::CalphaBuild::cluster(const std::vector<coot::scored_skel_coord>&, const clipper::Coord_orth&) const':
CalphaBuild.cc:317:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<interesting.size(); i++) {
                                     ^
CalphaBuild.cc:321:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<sum_centres.size(); j++) {
                                        ^
CalphaBuild.cc:340:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int j=0; j<sum_centres.size(); j++) {
                                     ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-cabuild.la -rpath /usr/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/CalphaBuild.o   ../angles/.libs/libcoot-AngleInfo.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so.0" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-cabuild.la" && ln -s "../libcoot-cabuild.la" "libcoot-cabuild.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o testcabuild testcabuild.o ./libcoot-cabuild.la ../angles/libcoot-AngleInfo.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/testcabuild testcabuild.o  ./.libs/libcoot-cabuild.so /builddir/build/BUILD/coot-0.7/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/build'
Making all in greg-tests
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/greg-tests'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/greg-tests'
Making all in python-tests
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/python-tests'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/python-tests'
Making all in analysis
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/analysis'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coot-utils -I../mini-mol -I../utils  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o bfkurt.lo bfkurt.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coot-utils -I../mini-mol -I../utils  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o mogul.lo mogul.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coot-utils -I../mini-mol -I../utils  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o bfactan.o bfactan.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coot-utils -I../mini-mol -I../utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c bfkurt.cc  -fPIC -DPIC -o .libs/bfkurt.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coot-utils -I../mini-mol -I../utils -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c mogul.cc  -fPIC -DPIC -o .libs/mogul.o
In file included from bfkurt.cc:6:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
bfkurt.cc: In constructor 'coot_extras::b_factor_analysis::b_factor_analysis(const CMMDBManager*, bool)':
bfkurt.cc:42:14: warning: unused variable 'seqnum' [-Wunused-variable]
          int seqnum = residue_p->GetSeqNum();
              ^
mogul.cc: In member function 'coot::mogul_item coot::mogul::parse_bond_line(const std::vector<std::basic_string<char> >&, const std::vector<std::basic_string<char> >&, const std::vector<std::basic_string<char> >&) const':
mogul.cc:95:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (md.counts.size() == md.n_bins) {
                              ^
mogul.cc: In constructor 'coot::mogul_distribution::mogul_distribution(const std::vector<std::basic_string<char> >&)':
mogul.cc:113:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int ibin=0; ibin<n_bins; ibin++) {
                                  ^
mogul.cc:115:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (ibit < bits.size()) {
                           ^
mogul.cc: In member function 'coot::dictionary_residue_restraints_t coot::mogul::make_restraints(const string&, const string&, const std::vector<std::basic_string<char> >&, int, int, const coot::dictionary_residue_restraints_t&)':
mogul.cc:260:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (idx_1 >= 0 && idx_1 < atom_names.size()) { 
                                                ^
mogul.cc:261:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (idx_2 >= 0 && idx_2 < atom_names.size()) {
                                                   ^
mogul.cc:279:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (idx_1 >= 0 && idx_1 < atom_names.size()) { 
                                                ^
mogul.cc:280:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (idx_2 >= 0 && idx_2 < atom_names.size()) {
                                                   ^
mogul.cc:281:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (idx_3 >= 0 && idx_3 < atom_names.size()) {
                                               ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-analysis.la -rpath /usr/lib bfkurt.lo mogul.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb    
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libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/bfactan bfactan.o  ./.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/analysis'
Making all in tw
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/tw'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o tw.lo tw.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o tiddly.o tiddly.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c tw.cc  -fPIC -DPIC -o .libs/tw.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-tw.la -rpath /usr/lib tw.lo  
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/tw.o   -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-tw.so.0 -o .libs/libcoot-tw.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-tw.so.0" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-tw.so" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-tw.la" && ln -s "../libcoot-tw.la" "libcoot-tw.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o coot-tiddly tiddly.o libcoot-tw.la  -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/coot-tiddly tiddly.o  ./.libs/libcoot-tw.so -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/tw'
Making all in libgtkgraph
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o annotation.lo annotation.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o polar_util.lo polar_util.c
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/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o axis.lo axis.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o gtkgraph.lo gtkgraph.c
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c annotation.c  -fPIC -DPIC -o .libs/annotation.o
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c polar_util.c  -fPIC -DPIC -o .libs/polar_util.o
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c trace.c  -fPIC -DPIC -o .libs/trace.o
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c axis.c  -fPIC -DPIC -o .libs/axis.o
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c gtkgraph.c  -fPIC -DPIC -o .libs/gtkgraph.o
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o polar.lo polar.c
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c polar.c  -fPIC -DPIC -o .libs/polar.o
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c -o smith.lo smith.c
libtool: compile:  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c smith.c  -fPIC -DPIC -o .libs/smith.o
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables  -Wl,-z,relro  -o libcoot-gtkgraph.la -rpath /usr/lib annotation.lo polar_util.lo trace.lo axis.lo gtkgraph.lo polar.lo smith.lo -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lm 
libtool: link: gcc -shared  -fPIC -DPIC  .libs/annotation.o .libs/polar_util.o .libs/trace.o .libs/axis.o .libs/gtkgraph.o .libs/polar.o .libs/smith.o   -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lm  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-gtkgraph.so.0 -o .libs/libcoot-gtkgraph.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so.0" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-gtkgraph.la" && ln -s "../libcoot-gtkgraph.la" "libcoot-gtkgraph.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
Making all in lbg
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/lbg'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg.lo lbg.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o wmolecule.lo wmolecule.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-search.lo lbg-search.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o residue-circles.lo residue-circles.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o flev-annotations.lo flev-annotations.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c residue-circles.cc  -fPIC -DPIC -o .libs/residue-circles.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c flev-annotations.cc  -fPIC -DPIC -o .libs/flev-annotations.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c wmolecule.cc  -fPIC -DPIC -o .libs/wmolecule.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lbg-search.cc  -fPIC -DPIC -o .libs/lbg-search.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lbg.cc  -fPIC -DPIC -o .libs/lbg.o
In file included from flev-annotations.cc:8:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from lbg.hh:53:0,
                 from residue-circles.cc:28:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:53:0,
                 from wmolecule.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:53:0,
                 from lbg.cc:49:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:53:0,
                 from lbg-search.cc:34:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-drag-and-drop.lo lbg-drag-and-drop.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c lbg-drag-and-drop.cc  -fPIC -DPIC -o .libs/lbg-drag-and-drop.o
In file included from lbg.hh:61:0,
                 from residue-circles.cc:28:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from lbg.hh:61:0,
                 from wmolecule.cc:33:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from lbg.hh:61:0,
                 from lbg-search.cc:34:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
residue-circles.cc: In constructor 'lbg_info_t::optimise_residue_circles::optimise_residue_circles(const std::vector<lbg_info_t::residue_circle_t>&, const std::vector<lbg_info_t::residue_circle_t>&, const widgeted_molecule_t&, const std::vector<int>&)':
residue-circles.cc:100:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    } while (status == GSL_CONTINUE && iter < n_steps);
                                              ^
residue-circles.cc: In static member function 'static double lbg_info_t::optimise_residue_circles::f(const gsl_vector*, void*)':
residue-circles.cc:287:10: warning: unused variable 'angle_penalty' [-Wunused-variable]
   double angle_penalty = k_angle_scale * exp(-2.5*one_minus_ct*one_minus_ct);
          ^
residue-circles.cc:210:11: warning: unused variable 'atom_scale' [-Wunused-variable]
    double atom_scale = 1.0;
           ^
residue-circles.cc: In static member function 'static void lbg_info_t::optimise_residue_circles::df(const gsl_vector*, void*, gsl_vector*)':
residue-circles.cc:327:11: warning: unused variable 'atom_scale' [-Wunused-variable]
    double atom_scale = 1.0;
           ^
In file included from lbg.hh:61:0,
                 from lbg.cc:49:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
wmolecule.cc: In member function 'GooCanvasItem* widgeted_atom_t::make_canvas_text_item(const lig_build::atom_id_info_t&, const string&, GooCanvasItem*)':
wmolecule.cc:217:18: warning: unused variable 'item' [-Wunused-variable]
   GooCanvasItem *item =
                  ^
wmolecule.cc: In member function 'GooCanvasItem* widgeted_bond_t::canvas_item_for_bond(const lig_build::pos_t&, const lig_build::pos_t&, bool, bool, lig_build::bond_t::bond_type_t, GooCanvasItem*) const':
wmolecule.cc:390:18: warning: unused variable 'ci_1' [-Wunused-variable]
   GooCanvasItem *ci_1 = wrap_goo_canvas_polyline_new_line(group,
                  ^
wmolecule.cc:393:18: warning: unused variable 'ci_2' [-Wunused-variable]
   GooCanvasItem *ci_2 = wrap_goo_canvas_polyline_new_line(group,
                  ^
wmolecule.cc:396:18: warning: unused variable 'ci_3' [-Wunused-variable]
   GooCanvasItem *ci_3 = wrap_goo_canvas_polyline_new_line(group,
                  ^
wmolecule.cc: In member function 'GooCanvasItem* widgeted_bond_t::canvas_item_double_bond(const lig_build::pos_t&, const lig_build::pos_t&, GooCanvasItem*) const':
wmolecule.cc:431:19: warning: unused variable 'ci_1' [-Wunused-variable]
    GooCanvasItem *ci_1 = wrap_goo_canvas_polyline_new_line(group,
                   ^
wmolecule.cc:434:19: warning: unused variable 'ci_2' [-Wunused-variable]
    GooCanvasItem *ci_2 = wrap_goo_canvas_polyline_new_line(group,
                   ^
wmolecule.cc: In member function 'GooCanvasItem* widgeted_bond_t::canvas_item_double_aromatic_bond(const lig_build::pos_t&, const lig_build::pos_t&, GooCanvasItem*) const':
wmolecule.cc:451:19: warning: unused variable 'ci_1' [-Wunused-variable]
    GooCanvasItem *ci_1 = wrap_goo_canvas_polyline_new_line(group,
                   ^
lbg-search.cc: In member function 'void lbg_info_t::search() const':
lbg-search.cc:43:14: warning: unused variable 'res' [-Wunused-variable]
    CResidue *res = 0;
              ^
wmolecule.cc:482:19: warning: unused variable 'ci_2' [-Wunused-variable]
    GooCanvasItem *ci_2 =
                   ^
wmolecule.cc: In member function 'GooCanvasItem* widgeted_bond_t::make_wedge_in_bond_item(const lig_build::pos_t&, const lig_build::pos_t&, GooCanvasItem*) const':
wmolecule.cc:568:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=1; i<=n_lines; i++) {
                              ^
wmolecule.cc:575:22: warning: unused variable 'ci_1' [-Wunused-variable]
       GooCanvasItem *ci_1 = wrap_goo_canvas_polyline_new_line(group,
                      ^
lbg-search.cc: In member function 'std::vector<lbg_info_t::match_results_t> lbg_info_t::compare_vs_sbase(CGraph*, float, int) const':
lbg-search.cc:204:7: warning: unused variable 'rc' [-Wunused-variable]
   int rc = SBase->GetGraph(graphFile, graph_2, exclude_H_flag);
       ^
wmolecule.cc: In member function 'bool widgeted_molecule_t::close_bond(int, GooCanvasItem*, bool)':
wmolecule.cc:884:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ((ib >= 0) && (ib<bonds.size())) {
                                    ^
lbg-search.cc: In member function 'lbg_info_t::match_results_t lbg_info_t::residue_from_best_match(CGraph&, CGraph&, CGraphMatch&, int, CSBStructure*) const':
lbg-search.cc:263:8: warning: unused variable 'best_match' [-Wunused-variable]
    int best_match = UNASSIGNED_INDEX;
        ^
wmolecule.cc: In member function 'bool widgeted_molecule_t::close_atom(int, GooCanvasItem*)':
wmolecule.cc:927:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ((iat >= 0) && (iat<atoms.size())) {
                                      ^
lbg-search.cc: In member function 'void lbg_info_t::display_search_results(std::vector<lbg_info_t::match_results_t>) const':
lbg-search.cc:349:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<v.size(); i++) {
                           ^
wmolecule.cc: In member function 'bool widgeted_molecule_t::write_minimal_cif_file(const string&) const':
wmolecule.cc:1208:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
          for (int i=0; i<atoms.size(); i++) {
                                     ^
wmolecule.cc:1225:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
          for (int i=0; i<bonds.size(); i++) {
                                     ^
wmolecule.cc:1157:9: warning: unused variable 'S' [-Wunused-variable]
    char S[2000];
         ^
lbg.cc: In function 'lbg_info_t* lbg(lig_build::molfile_molecule_t, std::pair<bool, coot::residue_spec_t>, CMMDBManager*, const string&, const string&, int, bool, bool, int (*)(const char*, const char*), void (*)(std::string), void (*)(std::string), std::string (*)(std::string))':
lbg.cc:144:7: warning: unused variable 'init_status' [-Wunused-variable]
   int init_status = lbg->init(NULL); // setup canvas, but not gui.
       ^
lbg.cc: In function 'bool on_canvas_button_press(GooCanvasItem*, GooCanvasItem*, GdkEventButton*, gpointer)':
lbg.cc:411:29: warning: unused variable 'spec_p' [-Wunused-variable]
       coot::residue_spec_t *spec_p =
                             ^
lbg.cc:385:9: warning: variable 'button_1_is_pressed' set but not used [-Wunused-but-set-variable]
    bool button_1_is_pressed = false;
         ^
lbg.cc: In function 'bool on_canvas_motion_new(GooCanvasItem*, GooCanvasItem*, GdkEventMotion*, gpointer)':
lbg.cc:524:8: warning: variable 'x_as_int' set but not used [-Wunused-but-set-variable]
    int x_as_int = -1, y_as_int = -1;
        ^
lbg.cc:524:23: warning: variable 'y_as_int' set but not used [-Wunused-but-set-variable]
    int x_as_int = -1, y_as_int = -1;
                       ^
lbg.cc:525:20: warning: unused variable 'state' [-Wunused-variable]
    GdkModifierType state;
                    ^
lbg.cc: In member function 'void lbg_info_t::rotate_latest_bond(int, int)':
lbg.cc:718:18: warning: unused variable 'root' [-Wunused-variable]
   GooCanvasItem *root = goo_canvas_get_root_item(GOO_CANVAS(canvas));
                  ^
lbg.cc:714:9: warning: unused variable 'debug' [-Wunused-variable]
    bool debug = 0;
         ^
lbg.cc: In member function 'void lbg_info_t::extend_latest_bond()':
lbg.cc:775:20: warning: unused variable 'bond' [-Wunused-variable]
   widgeted_bond_t &bond = mol.bonds.back();
                    ^
lbg.cc:776:20: warning: unused variable 'atom' [-Wunused-variable]
   widgeted_atom_t &atom = mol.atoms.back();
                    ^
lbg.cc: In member function 'void lbg_info_t::remove_bond_and_atom_highlighting()':
lbg.cc:834:19: warning: unused variable 'root' [-Wunused-variable]
    GooCanvasItem *root = goo_canvas_get_root_item (GOO_CANVAS(canvas));
                   ^
lbg.cc: In member function 'bool lbg_info_t::change_atom_element(int, std::string, std::string)':
lbg.cc:1146:21: warning: variable 'pos' set but not used [-Wunused-but-set-variable]
    lig_build::pos_t pos = mol.atoms[atom_index].atom_position;
                     ^
wmolecule.cc: In member function 'int topological_equivalence_t::assign_invariant_sequence_number(const std::vector<long int>&, const std::vector<std::pair<int, int> >&, int)':
wmolecule.cc:1864:29: warning: unused variable 'bond' [-Wunused-variable]
      const widgeted_bond_t &bond = bonds[atom_indices_inner[ivi].second];
                             ^
lbg.cc: In member function 'void lbg_info_t::add_bond_to_atom_with_3_neighbours(int, int, const std::vector<int>&)':
lbg.cc:1523:11: warning: unused variable 'l' [-Wunused-variable]
       int l = attached_bonds.size();
           ^
lbg.cc: In member function 'lig_build::pos_t lbg_info_t::get_new_pos_not_towards_ring_centres(int, const std::vector<int>&) const':
lbg.cc:1710:23: warning: variable 'ring_centre' set but not used [-Wunused-but-set-variable]
      lig_build::pos_t ring_centre = mol.bonds[bond_indices[i]].centre_pos();
                       ^
lbg.cc: In member function 'lig_build::pos_t lbg_info_t::new_pos_by_bisection(int, const std::vector<int>&, const std::vector<double>&, GooCanvasItem*) const':
lbg.cc:1738:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == bond_indices.size())
                                  ^
lbg.cc: In member function 'std::vector<double> lbg_info_t::get_angles(int, const std::vector<int>&) const':
lbg.cc:1769:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == bond_indices.size())
                                  ^
lbg.cc: In member function 'void lbg_info_t::try_stamp_bond_anywhere(int, int, int)':
lbg.cc:1976:9: warning: unused variable 'changed_status' [-Wunused-variable]
    bool changed_status = 0;
         ^
lbg.cc: In member function 'std::vector<int> lbg_info_t::stamp_polygon(int, lig_build::polygon_position_info_t, bool, GooCanvasItem*)':
lbg.cc:2057:18: warning: unused variable 'rect_item' [-Wunused-variable]
   GooCanvasItem *rect_item  =
                  ^
lbg.cc:2070:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == atom_pos_index.size())
                                    ^
lbg.cc: In member function 'lig_build::polygon_position_info_t lbg_info_t::highlight_data_t::get_new_polygon_centre_using_2_atoms(int, const double&) const':
lbg.cc:2150:11: warning: unused variable 'x_cen' [-Wunused-variable]
    double x_cen = 0;
           ^
lbg.cc:2151:11: warning: unused variable 'y_cen' [-Wunused-variable]
    double y_cen = 0;
           ^
lbg.cc: In member function 'lig_build::polygon_position_info_t lbg_info_t::highlight_data_t::get_new_polygon_centre_using_1_atom(int, bool, const double&, const double&, const widgeted_molecule_t&) const':
lbg.cc:2273:20: warning: variable 'bond_vector' set but not used [-Wunused-but-set-variable]
   lig_build::pos_t bond_vector = neighbours[1] - neighbours[0];
                    ^
lbg.cc: In member function 'bool lbg_info_t::init(GtkBuilder*)':
lbg.cc:2515:11: warning: unused variable 'timeout_handle' [-Wunused-variable]
       int timeout_handle = gtk_timeout_add(500, watch_for_mdl_from_coot, this);
           ^
lbg.cc: In member function 'void lbg_info_t::ligand_grid::add_quadratic(const std::vector<std::pair<lig_build::pos_t, double> >&)':
lbg.cc:3596:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int ix=0; ix<x_size(); ix++) {
                                     ^
lbg.cc:3597:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iy=0; iy<y_size(); iy++) {
                                        ^
lbg.cc: In member function 'lig_build::pos_t lbg_info_t::ligand_grid::find_minimum_position() const':
lbg.cc:3614:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ix=0; ix<x_size(); ix++) {
                                      ^
lbg.cc:3615:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iy=0; iy<y_size(); iy++) {
                                         ^
lbg.cc: In member function 'std::pair<lbg_info_t::grid_index_t, lig_build::pos_t> lbg_info_t::ligand_grid::find_nearest_zero(const lig_build::pos_t&, const std::vector<lbg_info_t::grid_index_t>&) const':
lbg.cc:3647:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int ix=0; ix<x_size(); ix++) {
                                     ^
lbg.cc:3648:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iy=0; iy<y_size(); iy++) {
                                        ^
lbg.cc: In constructor 'lbg_info_t::contour_fragment::contour_fragment(int, const float&, const lbg_info_t::grid_index_t&, const lbg_info_t::grid_index_t&, const lbg_info_t::ligand_grid&)':
lbg.cc:3831:8: warning: unused variable 'ii_next' [-Wunused-variable]
    int ii_next = lbg_info_t::grid_index_t::INVALID_INDEX;
        ^
lbg.cc:3832:8: warning: unused variable 'jj_next' [-Wunused-variable]
    int jj_next = lbg_info_t::grid_index_t::INVALID_INDEX;
        ^
lbg.cc: In member function 'void lbg_info_t::show_grid(const lbg_info_t::ligand_grid&)':
lbg.cc:4066:19: warning: unused variable 'rect' [-Wunused-variable]
    GooCanvasItem *rect =
                   ^
lbg.cc: In member function 'void lbg_info_t::ligand_grid::show_contour(GooCanvasItem*, float, const std::vector<widgeted_atom_ring_centre_info_t>&, const std::vector<std::vector<std::basic_string<char> > >&) const':
lbg.cc:4174:26: warning: variable 'pos_1' set but not used [-Wunused-but-set-variable]
         lig_build::pos_t pos_1 = to_canvas_pos(xy_1.first, xy_1.second);
                          ^
lbg.cc:4175:26: warning: variable 'pos_2' set but not used [-Wunused-but-set-variable]
         lig_build::pos_t pos_2 = to_canvas_pos(xy_2.first, xy_2.second);
                          ^
lbg.cc:4134:8: warning: unused variable 'ii' [-Wunused-variable]
    int ii=0;
        ^
lbg.cc:4135:8: warning: unused variable 'jj' [-Wunused-variable]
    int jj=0;
        ^
lbg.cc: In member function 'void lbg_info_t::ligand_grid::plot_contour_lines(const std::vector<std::vector<lig_build::pos_t> >&, GooCanvasItem*) const':
lbg.cc:4323:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<(contour_lines[i].size()-1); j++) {
                                                 ^
lbg.cc: In member function 'void lbg_info_t::show_mol_ring_centres()':
lbg.cc:4349:22: warning: unused variable 'rect_item' [-Wunused-variable]
       GooCanvasItem *rect_item = goo_canvas_rect_new (root,
                      ^
lbg.cc: In member function 'void lbg_info_t::show_unlimited_atoms(const std::vector<widgeted_atom_ring_centre_info_t>&)':
lbg.cc:4363:22: warning: unused variable 'rect_item' [-Wunused-variable]
       GooCanvasItem *rect_item =
                      ^
lbg.cc: In member function 'void lbg_info_t::show_ring_centres(std::vector<std::vector<std::basic_string<char> > >, const widgeted_molecule_t&)':
lbg.cc:4383:18: warning: unused variable 'rect_item' [-Wunused-variable]
   GooCanvasItem *rect_item =
                  ^
lbg.cc: In member function 'std::string lbg_info_t::grid_intensity_to_colour(int) const':
lbg.cc:4410:8: warning: unused variable 'step' [-Wunused-variable]
    int step = 8;
        ^
lbg.cc: In constructor 'lbg_info_t::ligand_grid::ligand_grid(const lig_build::pos_t&, const lig_build::pos_t&)':
lbg.cc:4491:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<x_size_; i++)
                             ^
lbg.cc: In member function 'void lbg_info_t::ligand_grid::add_for_accessibility_no_bash_dist_atom(double, const lig_build::pos_t&)':
lbg.cc:4592:9: warning: unused variable 'debug' [-Wunused-variable]
    bool debug = 1;
         ^
lbg.cc: In member function 'std::pair<int, std::vector<lbg_info_t::residue_circle_t> > lbg_info_t::optimise_residue_circle_positions(const std::vector<lbg_info_t::residue_circle_t>&, const std::vector<lbg_info_t::residue_circle_t>&, const std::vector<int>&) const':
lbg.cc:4658:7: warning: unused variable 'status' [-Wunused-variable]
   int status = orc.get_gsl_min_status();
       ^
lbg.cc: In member function 'std::vector<lbg_info_t::residue_circle_t> lbg_info_t::read_residues(const string&) const':
lbg.cc:4766:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int iat=0; iat<n_atoms_max; iat++) {
                                      ^
lbg.cc:4768:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (l > (name_index+4)) {
                          ^
lbg.cc: In member function 'void lbg_info_t::draw_residue_circles(const std::vector<lbg_info_t::residue_circle_t>&, const std::vector<int>&)':
lbg.cc:4828:23: warning: variable 'pos' set but not used [-Wunused-but-set-variable]
      lig_build::pos_t pos = l_residue_circles[i].pos;
                       ^
lbg.cc:4813:11: warning: unused variable 'max_dist_water_to_ligand_atom' [-Wunused-variable]
    double max_dist_water_to_ligand_atom  = 3.3; // don't draw waters that are far from ligand
           ^
lbg.cc:4814:11: warning: unused variable 'max_dist_water_to_protein_atom' [-Wunused-variable]
    double max_dist_water_to_protein_atom = 3.3; // don't draw waters that are not somehow 
           ^
lbg.cc: In member function 'void lbg_info_t::draw_solvent_exposure_circle(const lbg_info_t::residue_circle_t&, const lig_build::pos_t&, GooCanvasItem*)':
lbg.cc:5081:21: warning: unused variable 'circle' [-Wunused-variable]
      GooCanvasItem *circle = goo_canvas_ellipse_new(group,
                     ^
lbg.cc: In member function 'void lbg_info_t::draw_solvent_accessibility_of_atom(const lig_build::pos_t&, double, GooCanvasItem*)':
lbg.cc:5209:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_circles; i++) { 
                                ^
lbg.cc:5211:18: warning: unused variable 'circle' [-Wunused-variable]
   GooCanvasItem *circle = goo_canvas_ellipse_new(root,
                  ^
lbg.cc: In member function 'void lbg_info_t::draw_annotated_stacking_line(const lig_build::pos_t&, const lig_build::pos_t&, int)':
lbg.cc:5550:18: warning: unused variable 'text_1' [-Wunused-variable]
   GooCanvasItem *text_1 = goo_canvas_text_new(group,
                  ^
lbg.cc:5476:13: warning: unused variable 'start_arrow' [-Wunused-variable]
    gboolean start_arrow = 0;
             ^
lbg.cc:5477:13: warning: unused variable 'end_arrow' [-Wunused-variable]
    gboolean end_arrow = 1;
             ^
lbg.cc:5564:19: warning: unused variable 'item_1' [-Wunused-variable]
    GooCanvasItem *item_1 =
                   ^
lbg.cc:5573:19: warning: unused variable 'item_2' [-Wunused-variable]
    GooCanvasItem *item_2 =
                   ^
lbg.cc: In member function 'void lbg_info_t::draw_bonds_to_ligand()':
lbg.cc:5669:24: warning: unused variable 'item' [-Wunused-variable]
         GooCanvasItem *item = goo_canvas_polyline_new_line(root,
                        ^
lbg.cc:5600:23: warning: unused variable 'dash_unbroken' [-Wunused-variable]
    GooCanvasLineDash *dash_unbroken = goo_canvas_line_dash_new (1, 3);
                       ^
lbg.cc: In member function 'void lbg_info_t::show_key()':
lbg.cc:5771:19: warning: unused variable 'item_1' [-Wunused-variable]
    GooCanvasItem *item_1 =
                   ^
lbg.cc:5780:19: warning: unused variable 'text_1' [-Wunused-variable]
    GooCanvasItem *text_1 = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5789:19: warning: unused variable 'item_2' [-Wunused-variable]
    GooCanvasItem *item_2 =
                   ^
lbg.cc:5799:19: warning: unused variable 'text_2' [-Wunused-variable]
    GooCanvasItem *text_2 = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5809:19: warning: unused variable 'item_3' [-Wunused-variable]
    GooCanvasItem *item_3 =
                   ^
lbg.cc:5819:19: warning: unused variable 'text_3' [-Wunused-variable]
    GooCanvasItem *text_3 = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5828:19: warning: unused variable 'item_4' [-Wunused-variable]
    GooCanvasItem *item_4 =
                   ^
lbg.cc:5838:19: warning: unused variable 'text_4' [-Wunused-variable]
    GooCanvasItem *text_4 = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5848:19: warning: unused variable 'item_5' [-Wunused-variable]
    GooCanvasItem *item_5 =
                   ^
lbg.cc:5857:19: warning: unused variable 'text_5' [-Wunused-variable]
    GooCanvasItem *text_5 = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5865:19: warning: unused variable 'item_6' [-Wunused-variable]
    GooCanvasItem *item_6 =
                   ^
lbg.cc:5874:19: warning: unused variable 'text_6' [-Wunused-variable]
    GooCanvasItem *text_6 = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5893:19: warning: unused variable 'circle_grease' [-Wunused-variable]
    GooCanvasItem *circle_grease = 
                   ^
lbg.cc:5899:19: warning: unused variable 'circle_polar' [-Wunused-variable]
    GooCanvasItem *circle_polar = 
                   ^
lbg.cc:5905:19: warning: unused variable 'circle_acidic' [-Wunused-variable]
    GooCanvasItem *circle_acidic = 
                   ^
lbg.cc:5912:19: warning: unused variable 'circle_basic' [-Wunused-variable]
    GooCanvasItem *circle_basic = 
                   ^
lbg.cc:5919:19: warning: unused variable 'circle_water' [-Wunused-variable]
    GooCanvasItem *circle_water = 
                   ^
lbg.cc:5925:19: warning: unused variable 'circle_metal' [-Wunused-variable]
    GooCanvasItem *circle_metal = 
                   ^
lbg.cc:5932:19: warning: unused variable 'text_grease' [-Wunused-variable]
    GooCanvasItem *text_grease = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5940:19: warning: unused variable 'text_polar' [-Wunused-variable]
    GooCanvasItem *text_polar = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5948:19: warning: unused variable 'text_acidic' [-Wunused-variable]
    GooCanvasItem *text_acidic = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5956:19: warning: unused variable 'text_basic' [-Wunused-variable]
    GooCanvasItem *text_basic = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5964:19: warning: unused variable 'text_water' [-Wunused-variable]
    GooCanvasItem *text_water = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5973:19: warning: unused variable 'text_metal' [-Wunused-variable]
    GooCanvasItem *text_metal = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5988:19: warning: unused variable 'text_solvent_atom' [-Wunused-variable]
    GooCanvasItem *text_solvent_atom = goo_canvas_text_new(key_group,
                   ^
lbg.cc:5998:19: warning: unused variable 'circle_residue_exposure_1' [-Wunused-variable]
    GooCanvasItem *circle_residue_exposure_1 = 
                   ^
lbg.cc:6004:19: warning: unused variable 'circle_residue_exposure_2' [-Wunused-variable]
    GooCanvasItem *circle_residue_exposure_2 = 
                   ^
lbg.cc:6010:19: warning: unused variable 'text_solvent_residue' [-Wunused-variable]
    GooCanvasItem *text_solvent_residue = goo_canvas_text_new(key_group,
                   ^
lbg.cc:6033:19: warning: unused variable 'text_substitution_contour' [-Wunused-variable]
    GooCanvasItem *text_substitution_contour = goo_canvas_text_new(key_group,
                   ^
In file included from lbg.hh:53:0,
                 from lbg-drag-and-drop.cc:11:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:61:0,
                 from lbg-drag-and-drop.cc:11:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
lbg-drag-and-drop.cc: In function 'void on_lbg_drag_data_received(GtkWidget*, GdkDragContext*, gint, gint, GtkSelectionData*, guint, guint, gpointer)':
lbg-drag-and-drop.cc:51:15: warning: unused variable 'canvas' [-Wunused-variable]
    GtkWidget *canvas = GTK_WIDGET(user_data);
               ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o qed-interface.lo qed-interface.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c qed-interface.cc  -fPIC -DPIC -o .libs/qed-interface.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o alerts.lo alerts.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c alerts.cc  -fPIC -DPIC -o .libs/alerts.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o alerts-list.lo alerts-list.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c alerts-list.cc  -fPIC -DPIC -o .libs/alerts-list.o
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lidia-main.o lidia-main.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc
In file included from lbg.hh:53:0,
                 from lidia-main.cc:44:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:53:0,
                 from lbg-callbacks.cc:31,
                 from lbg-callbacks-outer.cc:2:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:61:0,
                 from lidia-main.cc:44:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from lbg.hh:61:0,
                 from lbg-callbacks.cc:31,
                 from lbg-callbacks-outer.cc:2:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
lbg.cc: At global scope:
lbg.cc:4846:1: warning: 'bool on_residue_circle_clicked(GooCanvasItem*, GooCanvasItem*, GdkEventButton*, gpointer)' defined but not used [-Wunused-function]
 on_residue_circle_clicked(GooCanvasItem  *item,
 ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-lidia.la -rpath /usr/lib lbg.lo wmolecule.lo lbg-search.lo residue-circles.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm  -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/lbg.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../coot-utils/.libs/libcoot-coord-utils.so ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-lidia.so.0" && ln -s "libcoot-lidia.so.0.0.0" "libcoot-lidia.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-lidia.so" && ln -s "libcoot-lidia.so.0.0.0" "libcoot-lidia.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-lidia.la" && ln -s "../libcoot-lidia.la" "libcoot-lidia.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,--export-dynamic -Wl,-z,relro  -o lidia lidia-main.o lbg-callbacks-outer.o ./libcoot-lidia.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm  -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -lutil 
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,--export-dynamic -Wl,-z -Wl,relro -o .libs/lidia lidia-main.o lbg-callbacks-outer.o -Wl,-export-dynamic  ./.libs/libcoot-lidia.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-coord-utils.so ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb -lgsl -lgslcblas -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lpthread -ldl -lm -lpython2.7 -lutil
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/lbg'
Making all in cootaneer
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/cootaneer'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o buccaneer-lib.lo buccaneer-lib.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o buccaneer-prot.lo buccaneer-prot.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o buccaneer-sequence.lo buccaneer-sequence.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cootaneer-sequence.lo cootaneer-sequence.cpp
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cootaneer-demo.o cootaneer-demo.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c buccaneer-sequence.cpp  -fPIC -DPIC -o .libs/buccaneer-sequence.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c buccaneer-prot.cpp  -fPIC -DPIC -o .libs/buccaneer-prot.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c cootaneer-sequence.cpp  -fPIC -DPIC -o .libs/cootaneer-sequence.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c buccaneer-lib.cpp  -fPIC -DPIC -o .libs/buccaneer-lib.o
buccaneer-sequence.cpp: In static member function 'static std::pair<double, std::pair<int, int> > Ca_sequence::sequence_score(const std::vector<std::vector<double> >&, const clipper::String&)':
buccaneer-sequence.cpp:117:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < scores.size(); r++ ) {
                                    ^
buccaneer-sequence.cpp:125:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < score.size(); r++ ) sccum[r+1] = sccum[r]+score[r];
                                   ^
buccaneer-sequence.cpp:131:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r1 = 0; r1 < sccum.size()-minseq; r1++ )
                                       ^
buccaneer-sequence.cpp:132:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int r2 = r1+minseq; r2 < sccum.size(); r2++ ) {
                                               ^
cootaneer-sequence.cpp: In member function 'std::pair<std::basic_string<char>, double> Coot_sequence::sequence_chain(const clipper::Xmap<float>&, const std::vector<std::pair<std::basic_string<char>, std::basic_string<char> > >&, CMMDBManager&, std::string)':
cootaneer-sequence.cpp:21:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int c = 0; c < sequence.size(); c++ ) {
                                      ^
buccaneer-sequence.cpp: In static member function 'static Score_list<clipper::String> Ca_sequence::sequence_match(const std::vector<std::vector<double> >&, const clipper::MMoleculeSequence&)':
buccaneer-sequence.cpp:199:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int j = 0; j < seqmut.size(); j++ ) {
                                      ^
cootaneer-sequence.cpp: In static member function 'static void Coot_sequence::write_targets(std::string, std::vector<LLK_map_target::Sampled>)':
cootaneer-sequence.cpp:102:7: warning: unused variable 'nt' [-Wunused-variable]
   int nt = 20;
       ^
buccaneer-sequence.cpp: In static member function 'static Score_list<clipper::String> Ca_sequence::sequence_chain(const MChain&, const clipper::Xmap<float>&, const std::vector<LLK_map_target::Sampled>&, const clipper::MMoleculeSequence&)':
buccaneer-sequence.cpp:234:29: warning: typedef 'Mm' locally defined but not used [-Wunused-local-typedefs]
   typedef clipper::MMonomer Mm;
                             ^
buccaneer-sequence.cpp: In static member function 'static void Ca_sequence::sequence_apply(clipper::MChain&, const clipper::String&)':
buccaneer-sequence.cpp:307:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( chain.size() != seq.length() ) clipper::Message::message( clipper::Message_fatal( "Sequence: internal error - length mismatch" ) );
                                   ^
buccaneer-sequence.cpp:342:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < regions.size(); i++ ) {
                                     ^
buccaneer-sequence.cpp: In member function 'bool Ca_sequence::operator()(clipper::MiniMol&, const clipper::MiniMol&, const clipper::Xmap<float>&, const std::vector<LLK_map_target>&, const clipper::MMoleculeSequence&)':
buccaneer-sequence.cpp:380:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int t = 0; t < llktarget.size(); t++ )
                                       ^
buccaneer-sequence.cpp:387:10: warning: unused variable 'score_cutoff' [-Wunused-variable]
   double score_cutoff = -20.0 * reliability_;  // min score
          ^
buccaneer-sequence.cpp:388:10: warning: unused variable 'screl_cutoff' [-Wunused-variable]
   double screl_cutoff =   0.3 * reliability_;  // min diff between 1st & 2nd
          ^
buccaneer-sequence.cpp:376:29: warning: typedef 'Mm' locally defined but not used [-Wunused-local-typedefs]
   typedef clipper::MMonomer Mm;
                             ^
buccaneer-sequence.cpp: In member function 'clipper::String Ca_sequence::format() const':
buccaneer-sequence.cpp:442:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int chn = 0; chn < history.size(); chn++ ) {
                                         ^
buccaneer-sequence.cpp: In member function 'void Ca_sequence::History::append(const Ca_sequence&)':
buccaneer-sequence.cpp:457:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < data.history.size(); i++ )
                                          ^
buccaneer-sequence.cpp: In member function 'clipper::String Ca_sequence::History::format(const clipper::MiniMol&) const':
buccaneer-sequence.cpp:465:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int h = 0; h < history.size(); h++ ) {
                                     ^
buccaneer-prot.cpp: In member function 'clipper::ftype Ca_chain::ramachandran_phi(const int&) const':
buccaneer-prot.cpp:52:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( resno-1 >= 0 && resno < chain.size() )
                                           ^
buccaneer-prot.cpp: In member function 'clipper::ftype Ca_chain::ramachandran_psi(const int&) const':
buccaneer-prot.cpp:61:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( resno >= 0 && resno+1 < chain.size() )
                                           ^
buccaneer-prot.cpp: In member function 'std::vector<ProteinLoop::CoordList<5> > ProteinLoop::rebuild5atoms(clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth) const':
buccaneer-prot.cpp:169:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int ipsi1 = 0; ipsi1 < ca2s.size(); ipsi1++ ) {
                                            ^
buccaneer-prot.cpp:177:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int iphi2 = 0; iphi2 < cc2s.size(); iphi2++ ) {
                                         ^
buccaneer-prot.cpp: In member function 'std::vector<ProteinLoop::CoordList<8> > ProteinLoop::rebuild8atoms(clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth) const':
buccaneer-prot.cpp:214:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int i = 0; i < r5.size(); i++ ) {
                               ^
buccaneer-prot.cpp: In static member function 'static std::pair<int, int> ProteinTools::chain_sequence_match(const clipper::String&, const clipper::MMoleculeSequence&)':
buccaneer-prot.cpp:280:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int res = 0; res < seq[chn].sequence().length(); res++ )
                                                         ^
buccaneer-prot.cpp:286:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < chnseq.size(); i++ )
                                    ^
buccaneer-prot.cpp:294:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int chn = 0; chn < seqs.size(); chn++ ) {
                                      ^
buccaneer-prot.cpp:298:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int i = 0; i < seqs[chn].length(); i++ )
                                             ^
buccaneer-prot.cpp:299:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if ( i-off >= 0 && i-off < chnseq.length() )
                                           ^
buccaneer-lib.cpp: In member function 'void LLK_map_target::search(clipper::Xmap<float>&, clipper::Xmap<int>&, clipper::Xmap<int>&, const clipper::Xmap<float>&, const std::vector<clipper::RTop_orth>&) const':
buccaneer-lib.cpp:219:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int op = 0; op < rtops.size(); op++ ) {
                                     ^
buccaneer-lib.cpp: In member function 'clipper::ftype LLK_map_target::Sampled::llk(const clipper::Xmap<float>&, const clipper::RTop_orth&) const':
buccaneer-lib.cpp:274:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < repxyz.size(); i++ ) {
                                    ^
buccaneer-lib.cpp: In member function 'clipper::ftype LLK_map_target::Sampled::correl(const clipper::Xmap<float>&, const clipper::RTop_orth&) const':
buccaneer-lib.cpp:285:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < repxyz.size(); i++ ) {
                                    ^
buccaneer-prot.cpp: In static member function 'static bool ProteinTools::chain_tidy(clipper::MiniMol&, const clipper::MiniMol&)':
buccaneer-prot.cpp:364:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( chn < labels1.length() ) {
                               ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcootaneer.la -rpath /usr/lib buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/buccaneer-lib.o .libs/buccaneer-prot.o .libs/buccaneer-sequence.o .libs/cootaneer-sequence.o   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcootaneer.so.0 -o .libs/libcootaneer.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcootaneer.so.0" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so.0")
libtool: link: (cd ".libs" && rm -f "libcootaneer.so" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so")
libtool: link: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o cootaneer-demo cootaneer-demo.o ./libcootaneer.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb    
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/cootaneer-demo cootaneer-demo.o  ./.libs/libcootaneer.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootaneer'
Making all in cootilus
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/cootilus'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o nucleicacid_db.lo nucleicacid_db.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o nautilus-tools.lo nautilus-tools.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o nautilus-ss-find.lo nautilus-ss-find.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o nautilus-join.lo nautilus-join.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o nautilus-target.lo nautilus-target.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c nautilus-ss-find.cpp  -fPIC -DPIC -o .libs/nautilus-ss-find.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c nautilus-join.cpp  -fPIC -DPIC -o .libs/nautilus-join.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c nautilus-target.cpp  -fPIC -DPIC -o .libs/nautilus-target.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c nautilus-tools.cpp  -fPIC -DPIC -o .libs/nautilus-tools.o
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c nucleicacid_db.cpp  -fPIC -DPIC -o .libs/nucleicacid_db.o
nautilus-ss-find.cpp: In member function 'void SSfind::prep_xmap(const clipper::Xmap<float>&, double)':
nautilus-ss-find.cpp:19:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < mapbox.size(); i++ ) {
                                    ^
nautilus-ss-find.cpp: In member function 'std::vector<SearchResult> SSfind::search(const std::vector<std::pair<clipper::Coord_orth, clipper::Coord_orth> >&, const std::vector<clipper::RTop_orth>&, double, double) const':
nautilus-ss-find.cpp:59:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < ops.size(); r++ ) {
                                 ^
nautilus-ss-find.cpp:62:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < target_cs.size(); i++ ) {
                                         ^
nautilus-ss-find.cpp:74:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rslts.size(); i++ ) rslts[i].trn = srctrn[i];
                                   ^
nautilus-ss-find.cpp:79:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rslts.size(); i++ ) {  // loop over map
                                   ^
nautilus-ss-find.cpp:86:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int r = 0; r < index_lists.size(); r++ ) {      // loop over rotns
                                             ^
nautilus-ss-find.cpp:95:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ( !( i < index_list.size() ) ) break;
                                ^
nautilus-ss-find.cpp:109:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < rslts.size(); i++ )
                                   ^
nautilus-tools.cpp: In static member function 'static clipper::MiniMol NucleicAcidTools::flag_chains(const clipper::MiniMol&)':
nautilus-tools.cpp:66:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int r = 1; r < flag.size()-1; r++ )
                                        ^
nautilus-tools.cpp: In static member function 'static clipper::RTop_orth NucleicAcidTools::symmetry_rtop(const std::vector<clipper::Coord_orth>&, clipper::Coord_orth&, const clipper::Spacegroup&, const clipper::Cell&)':
nautilus-tools.cpp:81:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int a = 0; a < cowrk.size(); a++ )
                                   ^
nautilus-tools.cpp:89:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int a = 0; a < cwrk.size(); a++ ) {
                                    ^
nautilus-tools.cpp: In static member function 'static bool NucleicAcidTools::symm_match(clipper::MiniMol&, const clipper::MiniMol&)':
nautilus-tools.cpp:139:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < atomr.size(); i++ ) {
                                   ^
nucleicacid_db.cpp: In member function 'bool NucleicAcidDB::Chain::is_continuous() const':
nucleicacid_db.cpp:448:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < dbmonomers.size()-1; i++ ) {
                                          ^
nucleicacid_db.cpp: In member function 'void NucleicAcidDB::Chain::transform(const clipper::RTop_orth&)':
nucleicacid_db.cpp:462:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < dbmonomers.size(); r++ )
                                        ^
nautilus-target.cpp: In member function 'void NucleicAcidTarget::init_stats(const clipper::Xmap<float>&, int)':
nautilus-target.cpp:27:53: warning: typedef 'MRI' locally defined but not used [-Wunused-local-typedefs]
   typedef clipper::Xmap<float>::Map_reference_index MRI;
                                                     ^
nautilus-tools.cpp:174:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int a = 0; a < atomw.size(); a++ ) {
                                       ^
nautilus-target.cpp: In member function 'double NucleicAcidTarget::radius() const':
nautilus-target.cpp:48:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < target_.size(); i++ ) {
                                     ^
nautilus-target.cpp:53:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int a = 0; a < coords.size(); a++ ) {
                                    ^
nautilus-target.cpp: In member function 'float NucleicAcidTarget::score_min(const clipper::Xmap<float>&, const clipper::RTop_orth&) const':
nautilus-target.cpp:65:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < target_.size(); i++ ) {
                                     ^
nautilus-target.cpp: In member function 'float NucleicAcidTarget::score_sum(const clipper::Xmap<float>&, const clipper::RTop_orth&) const':
nautilus-target.cpp:77:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < target_.size(); i++ ) {
                                     ^
nautilus-tools.cpp:192:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for ( int a = 0; a < atomw.size(); a++ ) {
                                      ^
nautilus-join.cpp: In static member function 'static std::vector<int> NucleicAcidJoin::best_chain(std::vector<NucleicAcidJoin::Node>&)':
nautilus-join.cpp:21:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < node_score.size(); i++ )
                                        ^
nautilus-join.cpp:31:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int j = 0; j < nodes[node].ptrs.size(); j++ ) {
                                                ^
nautilus-join.cpp:57:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 1; i < node_score.size(); i++ )
                                        ^
nautilus-target.cpp: In member function 'const clipper::MiniMol NucleicAcidTargets::find(const clipper::Xmap<float>&, const clipper::MiniMol&, int, int, double)':
nautilus-target.cpp:452:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < found_s.size(); i++ ) {
                                     ^
nautilus-target.cpp:458:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int i = 0; i < found_p.size(); i++ ) {
                                     ^
nautilus-join.cpp: In static member function 'static clipper::MiniMol NucleicAcidJoin::join(const clipper::MiniMol&)':
nautilus-join.cpp:103:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < nas.size(); r++ ) {
                                 ^
nautilus-join.cpp:114:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r = 0; r < nas.size(); r++ ) equivalent[r] = r;
                                 ^
nautilus-join.cpp:128:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int i = 0; i < atoms.size(); i++ ) { // find other equivalent NAs
                                     ^
nautilus-join.cpp:155:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int r1 = 0; r1 < nas.size()-1; r1++ ) {
                                     ^
nautilus-target.cpp: In member function 'const clipper::MiniMol NucleicAcidTargets::prune(const clipper::MiniMol&) const':
nautilus-target.cpp:577:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for ( int i = 0; i < atoms.size(); i++ ) {
                                    ^
nautilus-join.cpp:167:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int i = 0; i < joins[e1].ptrs.size(); i++ )
                                           ^
nautilus-target.cpp: In member function 'const clipper::MiniMol NucleicAcidTargets::rebuild_bases(const clipper::Xmap<float>&, const clipper::MiniMol&) const':
nautilus-target.cpp:718:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for ( int i = 0; i < atoms.size(); i++ ) {
                                      ^
nautilus-join.cpp:194:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int r = 0; r < chn.size(); r++ )
                                   ^
nautilus-join.cpp:197:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f = 0; f < joins.size(); f++ )
                                     ^
nautilus-join.cpp:201:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int f = 0; f < joins.size(); f++ )
                                     ^
nautilus-join.cpp:216:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int c = 0; c < chns.size(); c++ ) {
                                  ^
nautilus-join.cpp:220:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for ( int r = 0; r < chns[c].size(); r++ ) {
                                       ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cootilus-build.lo cootilus-build.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c cootilus-build.cpp  -fPIC -DPIC -o .libs/cootilus-build.o
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cootilus-demo.o cootilus-demo.cpp
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcootilus.la -rpath /usr/lib nucleicacid_db.lo nautilus-tools.lo nautilus-ss-find.lo nautilus-join.lo nautilus-target.lo cootilus-build.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/nucleicacid_db.o .libs/nautilus-tools.o .libs/nautilus-ss-find.o .libs/nautilus-join.o .libs/nautilus-target.o .libs/cootilus-build.o   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcootilus.so.0 -o .libs/libcootilus.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcootilus.so.0" && ln -s "libcootilus.so.0.0.0" "libcootilus.so.0")
libtool: link: (cd ".libs" && rm -f "libcootilus.so" && ln -s "libcootilus.so.0.0.0" "libcootilus.so")
libtool: link: ( cd ".libs" && rm -f "libcootilus.la" && ln -s "../libcootilus.la" "libcootilus.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o cootilus-demo cootilus-demo.o ./libcootilus.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb    
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/cootilus-demo cootilus-demo.o  ./.libs/libcootilus.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootilus'
Making all in goograph
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/goograph'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../utils -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz            -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o goograph.lo goograph.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../utils -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/mmdb -I/usr/include/ssm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c goograph.cc  -fPIC -DPIC -o .libs/goograph.o
In file included from goograph.hh:32:0,
                 from goograph.cc:24:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from goograph.cc:24:0:
goograph.hh: In member function 'bool coot::goograph::is_valid_trace(int)':
goograph.hh:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (trace_id >= traces.size()) {
                                  ^
goograph.cc: In member function 'void coot::goograph::plot_line_graph(int)':
goograph.cc:665:12: warning: unused variable 'dashed' [-Wunused-variable]
       bool dashed = traces[trace_id].dashed;
            ^
goograph.cc: In member function 'void coot::goograph::plot_smoothed_line_graph(int)':
goograph.cc:710:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == (n_points-2))
                           ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o libcoot-goograph.la -rpath /usr/lib goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/goograph.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-goograph.so.0" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-goograph.so" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-goograph.la" && ln -s "../libcoot-goograph.la" "libcoot-goograph.la" )
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/goograph'
Making all in src
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/src'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o main.o main.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o svn-revision.o svn-revision.cc
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c c-inner-main.c
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-analysis.o c-interface-analysis.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-build.o c-interface-build.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-build-gui.o c-interface-build-gui.cc
c-inner-main.c: In function 'c_inner_main':
c-inner-main.c:286:6: warning: implicit declaration of function 'handle_command_line_data' [-Wimplicit-function-declaration]
      handle_command_line_data(closure);
      ^
c-inner-main.c:119:7: warning: unused variable 'preferences_dir_status' [-Wunused-variable]
   int preferences_dir_status;
       ^
c-inner-main.c:103:9: warning: unused variable 'preferences_filename' [-Wunused-variable]
   char *preferences_filename = ".coot-preferences.scm";
         ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-database.o c-interface-database.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-gui.o c-interface-gui.cc
In file included from ../goograph/goograph.hh:32:0,
                 from c-interface-analysis.cc:27:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from c-interface-analysis.cc:27:0:
../goograph/goograph.hh: In member function 'bool coot::goograph::is_valid_trace(int)':
../goograph/goograph.hh:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (trace_id >= traces.size()) {
                                  ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-build.cc:52:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lbg/lbg.hh:53:0,
                 from main.cc:61:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from c-interface-analysis.cc:30:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lbg/lbg.hh:61:0,
                 from main.cc:61:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from c-interface-scm.hh:32:0,
                 from c-interface-gui.cc:61:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-build.cc:68:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-build-gui.cc:58:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-build-gui.cc:64:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-gui.cc:68:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
c-interface-build.cc: In function 'int add_ligand_delete_residue_copy_molecule(int, const char*, int, int, const char*, int)':
c-interface-build.cc:339:12: warning: unused variable 'at' [-Wunused-variable]
     CAtom *at;
            ^
main.cc: In function 'int main(int, char**)':
main.cc:229:6: warning: 'void g_type_init()' is deprecated (declared at /usr/include/glib-2.0/gobject/gtype.h:669) [-Wdeprecated-declarations]
      g_type_init(); // for lbg command-line mode, so that
      ^
main.cc:229:18: warning: 'void g_type_init()' is deprecated (declared at /usr/include/glib-2.0/gobject/gtype.h:669) [-Wdeprecated-declarations]
      g_type_init(); // for lbg command-line mode, so that
                  ^
main.cc:636:16: warning: unused variable 'w' [-Wunused-variable]
     GtkWidget *w;
                ^
main.cc: In function 'int get_max_effective_screen_height()':
main.cc:740:18: warning: unused variable 'x' [-Wunused-variable]
             gint x = data[0];
                  ^
main.cc:741:18: warning: unused variable 'y' [-Wunused-variable]
             gint y = data[1];
                  ^
main.cc:717:10: warning: variable 'width' set but not used [-Wunused-but-set-variable]
     gint width;
          ^
main.cc: In function 'void setup_application_icon(GtkWindow*)':
main.cc:827:4: warning: 'void gdk_pixbuf_unref(GdkPixbuf*)' is deprecated (declared at /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf-core.h:243): Use 'g_object_unref' instead [-Wdeprecated-declarations]
    gdk_pixbuf_unref (icon_pixbuf);
    ^
main.cc:827:33: warning: 'void gdk_pixbuf_unref(GdkPixbuf*)' is deprecated (declared at /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf-core.h:243): Use 'g_object_unref' instead [-Wdeprecated-declarations]
    gdk_pixbuf_unref (icon_pixbuf);
                                 ^
main.cc:865:12: warning: unused variable 'stock_ids' [-Wunused-variable]
    GSList* stock_ids = gtk_stock_list_ids();
            ^
c-interface-build.cc: In function 'std::vector<coot::residue_spec_t> scm_to_residue_specs(SCM)':
c-interface-build.cc:1405:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<r_length; i++) {
                             ^
c-interface-build.cc: In function 'std::vector<coot::residue_spec_t> py_to_residue_specs(PyObject*)':
c-interface-build.cc:1516:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i<r_length; i++) {
                            ^
c-interface-build.cc: In function 'float auto_fit_best_rotamer(int, const char*, const char*, const char*, int, int, int, float)':
c-interface-build.cc:2059:16: warning: unused variable 'auto_range' [-Wunused-variable]
      short int auto_range = 1;
                ^
c-interface-build.cc: In function 'void write_header_secondary_structure_info(int, const char*)':
c-interface-build.cc:2931:7: warning: unused variable 'n_models' [-Wunused-variable]
   int n_models = mol->GetNumberOfModels();
       ^
c-interface-build.cc: In function 'int quick_save()':
c-interface-build.cc:3137:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imol=0; imol<graphics_n_molecules(); imol++) {
                                                        ^
c-interface-build.cc: In function 'scm_unused_struct* get_refmac_sad_atom_info_scm()':
c-interface-build.cc:3483:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<sad_atoms.size(); i++) {
                                  ^
c-interface-build.cc: In function 'PyObject* get_refmac_sad_atom_info_py()':
c-interface-build.cc:3520:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<sad_atoms.size(); i++) {
                                  ^
c-interface-analysis.cc: In function 'void hole(int, float, float, float, float, float, float, float, float, int, bool)':
c-interface-analysis.cc:82:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) {
                                ^
c-interface-analysis.cc:97:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i<n; i++) {
                            ^
c-interface-analysis.cc: In function 'void show_hole_probe_radius_graph_basic(const std::vector<std::pair<clipper::Coord_orth, double> >&, double)':
c-interface-analysis.cc:155:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n; i++) {
                             ^
c-interface-analysis.cc: In function 'void show_hole_probe_radius_graph_goocanvas(const std::vector<std::pair<clipper::Coord_orth, double> >&, double)':
c-interface-analysis.cc:186:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) {
                                ^
c-interface-build.cc: In function 'int new_molecule_by_symmetry(int, const char*, double, double, double, double, double, double, double, double, double, double, double, double, int, int, int)':
c-interface-build.cc:4654:38: warning: variable 'cell_info' set but not used [-Wunused-but-set-variable]
       std::pair<bool, clipper::Cell> cell_info = graphics_info_t::molecules[imol].cell();
                                      ^
c-interface-build.cc: In function 'scm_unused_struct* rigid_body_refine_by_residue_ranges_scm(int, SCM)':
c-interface-build.cc:5919:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int irange=0; irange<rr_length; irange++) {
                                      ^
c-interface-build.cc: In function 'PyObject* rigid_body_refine_by_residue_ranges_py(int, PyObject*)':
c-interface-build.cc:5976:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int irange=0; irange<rr_length; irange++) {
                                      ^
c-interface-build.cc: In function 'PyObject* protein_db_loops_py(int, PyObject*, int, int)':
c-interface-build.cc:7103:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i< p.second.size(); i++)
                                      ^
c-interface-build-gui.cc: In function 'void do_mutate_sequence(GtkWidget*)':
c-interface-build-gui.cc:1524:8: warning: variable 'swap_flag' set but not used [-Wunused-but-set-variable]
    int swap_flag = 0;
        ^
c-interface-build-gui.cc: In function 'void fit_loop_from_widget(GtkWidget*)':
c-interface-build-gui.cc:1699:14: warning: variable 'autofit_flag' set but not used [-Wunused-but-set-variable]
    short int autofit_flag = 0;
              ^
c-interface-gui.cc: In function 'void handle_column_label_make_fourier(GtkWidget*)':
c-interface-gui.cc:414:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (icol < saved_f_phi_columns->weight_cols.size())
                                                   ^
c-interface-gui.cc:349:15: warning: variable 'fobs_menu' set but not used [-Wunused-but-set-variable]
    GtkWidget *fobs_menu;
               ^
c-interface-gui.cc:350:15: warning: variable 'sigfobs_menu' set but not used [-Wunused-but-set-variable]
    GtkWidget *sigfobs_menu;
               ^
c-interface-gui.cc:351:15: warning: variable 'r_free_menu' set but not used [-Wunused-but-set-variable]
    GtkWidget *r_free_menu;
               ^
c-interface-gui.cc: In function 'void coot_real_exit(int)':
c-interface-gui.cc:1340:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imol=0; imol<graphics_n_molecules(); imol++)
                                                        ^
c-interface-gui.cc: In function 'void add_save_coordinates_include_hydrogens_and_aniso_checkbutton(GtkWidget*)':
c-interface-gui.cc:1431:18: warning: unused variable 'aa' [-Wunused-variable]
       GtkWidget *aa = GTK_FILE_SELECTION(fileselection)->action_area;
                  ^
c-interface-gui.cc: In function 'void add_filechooser_filter_button(GtkWidget*, short int)':
c-interface-gui.cc:1474:7: warning: unused variable 'i' [-Wunused-variable]
   int i = 0;
       ^
c-interface-gui.cc: In function 'void add_recentre_on_read_pdb_checkbutton(GtkWidget*)':
c-interface-gui.cc:1942:16: warning: unused variable 'tooltips' [-Wunused-variable]
   GtkTooltips *tooltips = gtk_tooltips_new();
                ^
c-interface-gui.cc: In function 'void set_refine_params_toggle_buttons(GtkWidget*)':
c-interface-gui.cc:2508:15: warning: unused variable 'link_torsion_type_vbox' [-Wunused-variable]
    GtkWidget *link_torsion_type_vbox =
               ^
c-interface-gui.cc: In function 'void show_model_toolbar_all_icons()':
c-interface-gui.cc:2788:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<(*graphics_info_t::model_toolbar_icons).size(); i++) {
                                                                ^
c-interface-gui.cc: In function 'void show_model_toolbar_main_icons()':
c-interface-gui.cc:2820:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<(*graphics_info_t::model_toolbar_icons).size(); i++) {
                                                                ^
c-interface-gui.cc: In function 'void update_toolbar_icons_menu(int)':
c-interface-gui.cc:2889:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<(toolbar_icons).size(); i++) {
                                        ^
c-interface-gui.cc: In function 'void free_memory_run_refmac(GtkWidget*)':
c-interface-gui.cc:3676:10: warning: variable 'imol_ptr' set but not used [-Wunused-but-set-variable]
    void *imol_ptr;
          ^
c-interface-gui.cc: In function 'void close_molecule_by_widget(GtkWidget*)':
c-interface-gui.cc:3865:19: warning: unused variable 'g' [-Wunused-variable]
   graphics_info_t g;
                   ^
c-interface-gui.cc: In function 'void fill_go_to_atom_window(GtkWidget*)':
c-interface-gui.cc:4847:17: warning: variable 'residue_gtklist' set but not used [-Wunused-but-set-variable]
      GtkWidget *residue_gtklist;
                 ^
c-interface-gui.cc:4848:13: warning: unused variable 'text' [-Wunused-variable]
      gchar *text; 
             ^
c-interface-gui.cc: In function 'GtkWidget* wrapped_create_add_additional_representation_gui()':
c-interface-gui.cc:5416:18: warning: unused variable 'chain_id_entry' [-Wunused-variable]
       GtkWidget *chain_id_entry = lookup_widget(w, "add_rep_chain_id_entry");
                  ^
c-interface-gui.cc:5417:18: warning: unused variable 'resno_start_entry' [-Wunused-variable]
       GtkWidget *resno_start_entry = lookup_widget(w, "add_rep_resno_start_entry");
                  ^
c-interface-gui.cc:5418:18: warning: unused variable 'resno_end_entry' [-Wunused-variable]
       GtkWidget *resno_end_entry = lookup_widget(w, "add_rep_resno_end_entry");
                  ^
c-interface-gui.cc:5419:18: warning: unused variable 'ins_code_entry' [-Wunused-variable]
       GtkWidget *ins_code_entry = lookup_widget(w, "add_rep_ins_code_entry");
                  ^
c-interface-gui.cc:5420:18: warning: unused variable 'string_selection_entry' [-Wunused-variable]
       GtkWidget *string_selection_entry = lookup_widget(w, "add_rep_selection_string_entry");
                  ^
c-interface-gui.cc:5422:18: warning: unused variable 'position_radiobutton' [-Wunused-variable]
       GtkWidget *position_radiobutton = lookup_widget(w, "add_rep_radiobutton_position");
                  ^
c-interface-gui.cc:5423:18: warning: unused variable 'resno_radiobutton' [-Wunused-variable]
       GtkWidget *resno_radiobutton = lookup_widget(w, "add_rep_radiobutton_res_number");
                  ^
c-interface-gui.cc:5424:18: warning: unused variable 'selection_string_radiobutton' [-Wunused-variable]
       GtkWidget *selection_string_radiobutton = lookup_widget(w, "add_rep_radiobutton_selection_string");
                  ^
c-interface-gui.cc:5426:18: warning: unused variable 'add_reps_fat_bonds_radiobutton' [-Wunused-variable]
       GtkWidget *add_reps_fat_bonds_radiobutton = lookup_widget(w, "add_rep_rep_fat_bonds_radiobutton");
                  ^
c-interface-gui.cc:5427:18: warning: unused variable 'add_reps_ball_and_stick_radiobutton' [-Wunused-variable]
       GtkWidget *add_reps_ball_and_stick_radiobutton = lookup_widget(w, "add_rep_rep_ball_and_stick_radiobutton");
                  ^
c-interface-gui.cc: In function 'void add_additional_representation_by_widget(GtkWidget*)':
c-interface-gui.cc:5450:15: warning: unused variable 'option_menu' [-Wunused-variable]
    GtkWidget *option_menu = lookup_widget(w, "add_rep_molecule_optionmenu");
               ^
c-interface-gui.cc:5462:15: warning: unused variable 'add_reps_fat_bonds_radiobutton' [-Wunused-variable]
    GtkWidget *add_reps_fat_bonds_radiobutton = lookup_widget(w, "add_rep_rep_fat_bonds_radiobutton");
               ^
c-interface-gui.cc: In function 'void show_restraints_editor_by_index(int)':
c-interface-gui.cc:5574:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i==menu_item_index)
              ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-gtk2.o c-interface-gtk2.cc
In file included from cc-interface.hh:28:0,
                 from c-interface-gtk2.cc:61:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-gtk2.cc:62:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-info.o c-interface-info.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-kk.o c-interface-kk.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-info.cc:64:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from c-interface-info.cc:67:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-kk.cc:31:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-kk.cc:31:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-ligands.o c-interface-ligands.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-ligands-gui.o c-interface-ligands-gui.cc
c-interface-info.cc: In function 'void edit_text(int, const char*)':
c-interface-info.cc:3102:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (text_handle < g.generic_texts_p->size()) {
                                             ^
c-interface-info.cc: In function 'PyObject* set_monomer_restraints_py(const char*, PyObject*)':
c-interface-info.cc:4173:11: warning: unused variable 'esd' [-Wunused-variable]
    float  esd            = PyFloat_AsDouble(esd_py);
           ^
c-interface-info.cc:4216:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i=1; i<atoms.size(); i++)
                                    ^
c-interface-info.cc: In function 'scm_unused_struct* remarks_scm(int)':
c-interface-info.cc:4581:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<l; i++) { 
                                ^
c-interface-info.cc: In function 'PyObject* remarks_py(int)':
c-interface-info.cc:4606:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_records; i++) {
                                ^
c-interface-kk.cc: In function 'PyObject* map_peaks_near_point_from_list_py(int, PyObject*, float, float, float, float)':
c-interface-kk.cc:44:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int peak_num=0; peak_num<l; peak_num++) {
                                              ^
c-interface-kk.cc: In function 'PyObject* regularize_zone_with_score_py(int, const char*, int, int, const char*)':
c-interface-kk.cc:236:8: warning: unused variable 'status' [-Wunused-variable]
    int status = 0;
        ^
c-interface-kk.cc: In function 'scm_unused_struct* regularize_zone_with_score_scm(int, const char*, int, int, const char*)':
c-interface-kk.cc:277:8: warning: unused variable 'status' [-Wunused-variable]
    int status = 0;
        ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-ligands.cc:46:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-ligands.cc:51:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-ligands-gui.cc:46:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
c-interface-ligands.cc: In function 'std::vector<int> execute_ligand_search_internal()':
c-interface-ligands.cc:646:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iclust=0; iclust<n_clusters; iclust++) {
                                       ^
c-interface-ligands.cc:669:12: warning: unused variable 'bf' [-Wunused-variable]
      float bf = graphics_info_t::default_new_atoms_b_factor;
            ^
c-interface-ligands.cc: In function 'PyObject* add_dipole_for_residues_py(int, PyObject*)':
c-interface-ligands.cc:1283:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int ispec=0; ispec<l; ispec++) {
                                        ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-ligands-gui.cc:49:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-maps.o c-interface-maps.cc
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from c-interface-maps.cc:30:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-maps.cc:38:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-mmdb.o c-interface-mmdb.cc
c-interface-maps.cc: In function 'int auto_read_make_and_draw_maps(const char*)':
c-interface-maps.cc:446:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for ( int ic = 0; ic < cols_f.size(); ic++ ) {
                                          ^
c-interface-maps.cc: In function 'PyObject* get_map_colour_py(int)':
c-interface-maps.cc:1133:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<colour_v.size(); i++) {
                                     ^
c-interface-maps.cc: In function 'int transform_map_raw(int, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, const char*, double, double, double, double, double, double)':
c-interface-maps.cc:1360:32: warning: variable 'mv' set but not used [-Wunused-but-set-variable]
       mean_and_variance<float> mv = map_density_distribution(new_map, 0);
                                ^
c-interface-maps.cc: In function 'int average_map_scm(SCM)':
c-interface-maps.cc:1408:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n; i++) {
                             ^
c-interface-maps.cc: In function 'int average_map_py(PyObject*)':
c-interface-maps.cc:1460:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n; i++) {
                             ^
c-interface-maps.cc: In function 'int make_variance_map_scm(SCM)':
c-interface-maps.cc:1541:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n; i++) { 
                             ^
c-interface-maps.cc: In function 'int make_variance_map_py(PyObject*)':
c-interface-maps.cc:1559:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) { 
                                ^
In file included from c-interface-python.hh:27:0,
                 from c-interface-mmdb.cc:36:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-mmdb.cc:40:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-mogul.o c-interface-mogul.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-mutate.o c-interface-mutate.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-mogul.cc:8:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-mogul.cc:8:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-mutate.cc:44:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-mutate.cc:44:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-ncs.o c-interface-ncs.cc
c-interface-mogul.cc: In function 'GtkWidget* wrapped_create_mogul_geometry_dialog(const coot::mogul&)':
c-interface-mogul.cc:126:17: warning: unused variable 'mogul_bonds_treeview' [-Wunused-variable]
    GtkTreeView *mogul_bonds_treeview    = GTK_TREE_VIEW(lookup_widget(w, "mogul_bonds_treeview"));
                 ^
c-interface-mogul.cc:127:17: warning: unused variable 'mogul_angles_treeview' [-Wunused-variable]
    GtkTreeView *mogul_angles_treeview   = GTK_TREE_VIEW(lookup_widget(w, "mogul_angles_treeview"));
                 ^
c-interface-mogul.cc:128:17: warning: unused variable 'mogul_torsions_treeview' [-Wunused-variable]
    GtkTreeView *mogul_torsions_treeview = GTK_TREE_VIEW(lookup_widget(w, "mogul_torsions_treeview"));
                 ^
c-interface-mutate.cc: In function 'int align_to_closest_chain(const char*, float)':
c-interface-mutate.cc:358:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imol=0; imol<graphics_n_molecules(); imol++) {
                                                        ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-network.o c-interface-network.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-nucleotides.o c-interface-nucleotides.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-ncs.cc:49:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-ncs.cc:52:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from cc-interface.hh:28:0,
                 from c-interface-network.cc:41:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-network.cc:46:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-nucleotides.cc:35:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-nucleotides.cc:35:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
c-interface-ncs.cc: In function 'void set_show_strict_ncs(int, int)':
c-interface-ncs.cc:192:14: warning: variable 'istate' set but not used [-Wunused-but-set-variable]
    short int istate = 0;
              ^
c-interface-network.cc: In function 'std::string coot_get_url_as_string_internal(const char*)':
c-interface-network.cc:147:13: warning: unused variable 'success' [-Wunused-variable]
    CURLcode success = curl_easy_perform(c);
             ^
c-interface-network.cc: In function 'scm_unused_struct* curl_progress_info(const char*)':
c-interface-network.cc:306:13: warning: unused variable 'liv' [-Wunused-variable]
    long int liv;
             ^
c-interface-network.cc: In function 'PyObject* curl_progress_info_py(const char*)':
c-interface-network.cc:343:13: warning: unused variable 'liv' [-Wunused-variable]
    long int liv;
             ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-python.o c-interface-python.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-pisa.o c-interface-pisa.cc
In file included from c-interface-python.hh:27:0,
                 from c-interface-python.cc:34:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-python.cc:36:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-pisa.cc:30:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-pisa.cc:30:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
c-interface-python.cc: In function 'clipper::Spacegroup py_symop_strings_to_space_group(PyObject*)':
c-interface-python.cc:123:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) {
                                ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-pisa-gui.o c-interface-pisa-gui.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-preferences.o c-interface-preferences.cc
c-interface-pisa.cc: In function 'scm_unused_struct* handle_pisa_interfaces_scm(SCM)':
c-interface-pisa.cc:132:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<interfaces_description_length; i++) {
                             ^
c-interface-pisa.cc: In function 'PyObject* handle_pisa_interfaces_py(PyObject*)':
c-interface-pisa.cc:316:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<interfaces_description_length; i++) {
                             ^
c-interface-pisa.cc: In function 'coot::pisa_interface_bond_info_t coot::get_pisa_interface_bond_info_scm(SCM)':
c-interface-pisa.cc:488:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ib=0; ib<bonds_info_length; ib++) {
                               ^
c-interface-pisa.cc: In function 'coot::pisa_interface_bond_info_t coot::get_pisa_interface_bond_info_py(PyObject*)':
c-interface-pisa.cc:520:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ib=0; ib<bonds_info_length; ib++) {
                               ^
c-interface-pisa.cc: In function 'clipper::Coord_orth make_complementary_dotted_surfaces(int, int, std::vector<coot::residue_spec_t>&, std::vector<coot::residue_spec_t>&)':
c-interface-pisa.cc:924:10: warning: unused variable 'close_dist' [-Wunused-variable]
    float close_dist = 4.3;
          ^
c-interface-pisa.cc: In function 'void pisa_interfaces_display_only(int, int, clipper::Coord_orth)':
c-interface-pisa.cc:975:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imol=0; imol<graphics_n_molecules(); imol++) {
                                                        ^
c-interface-pisa.cc:977:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ((imol != imol_1) && (imol != imol_2)) {
                ^
c-interface-pisa.cc:977:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ((imol != imol_1) && (imol != imol_2)) {
                                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-pisa-gui.cc:29:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-pisa-gui.cc:29:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-preferences.cc:59:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-preferences.cc:59:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-refine.o c-interface-refine.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-residues.o c-interface-residues.cc
c-interface-preferences.cc: In function 'void preferences()':
c-interface-preferences.cc:67:14: warning: unused variable 'w' [-Wunused-variable]
   GtkWidget *w;
              ^
c-interface-preferences.cc: In function 'void show_preferences()':
c-interface-preferences.cc:99:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j<fonts.size(); j++) {
                              ^
c-interface-preferences.cc: In function 'void show_hide_preferences_tabs(GtkToggleToolButton*, int)':
c-interface-preferences.cc:149:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<preferences_tabs.size(); i++) {
                                         ^
c-interface-preferences.cc: In function 'void update_preference_gui()':
c-interface-preferences.cc:207:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<g.preferences_internal.size(); i++) {
                                               ^
c-interface-preferences.cc:193:16: warning: unused variable 'gtext' [-Wunused-variable]
   const gchar *gtext;
                ^
c-interface-preferences.cc: In function 'void save_preferences()':
c-interface-preferences.cc:697:13: warning: variable 'istat' set but not used [-Wunused-but-set-variable]
   short int istat = 1;
             ^
c-interface-preferences.cc: In function 'void generic_object_info()':
c-interface-preferences.cc:1109:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<n_obs; i++) {
                       ^
c-interface-preferences.cc: In function 'short int generic_object_has_objects_p(int)':
c-interface-preferences.cc:1131:74: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ((object_number >=0) && (object_number < g.generic_objects_p->size())) {
                                                                          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-refine.cc:37:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-refine.cc:37:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from cc-interface.hh:28:0,
                 from c-interface-residues.cc:32:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-residues.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-scm.o c-interface-scm.cc
c-interface-refine.cc: In function 'PyObject* list_extra_restraints_py(int)':
c-interface-refine.cc:498:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int ib=0; ib<g.molecules[imol].extra_restraints.bond_restraints.size(); ib++) {
                                                                             ^
c-interface-refine.cc:514:78: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int it=0; it<g.molecules[imol].extra_restraints.angle_restraints.size(); it++) {
                                                                              ^
c-interface-refine.cc:533:80: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int it=0; it<g.molecules[imol].extra_restraints.torsion_restraints.size(); it++) {
                                                                                ^
c-interface-refine.cc:557:82: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int is=0; is<g.molecules[imol].extra_restraints.start_pos_restraints.size(); is++) {
                                                                                  ^
In file included from c-interface-scm.hh:32:0,
                 from c-interface-scm.cc:31:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-sfs.o c-interface-sfs.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-scm.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
c-interface-scm.cc: In function 'clipper::Spacegroup scm_symop_strings_to_space_group(SCM)':
c-interface-scm.cc:134:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) {
                                ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-superpose.o c-interface-superpose.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-validate.o c-interface-validate.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-view.o c-interface-view.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-superpose.cc:35:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-superpose.cc:35:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-validate.cc:48:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-widgets.o c-interface-widgets.cc
In file included from cc-interface.hh:28:0,
                 from c-interface-view.cc:30:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-validate.cc:51:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
c-interface-superpose.cc: In function 'void superpose(int, int, short int)':
c-interface-superpose.cc:85:11: warning: unused variable 'success' [-Wunused-variable]
      bool success = coot::util::copy_cell_and_symm_headers(m1, m2);
           ^
c-interface-superpose.cc: In function 'void superpose_with_chain_selection(int, int, const char*, const char*, int, int, short int)':
c-interface-superpose.cc:164:11: warning: unused variable 'success' [-Wunused-variable]
      bool success = coot::util::copy_cell_and_symm_headers(m1, m2);
           ^
c-interface-superpose.cc: In function 'int superpose_with_atom_selection(int, int, const char*, const char*, short int)':
c-interface-superpose.cc:232:12: warning: unused variable 'a' [-Wunused-variable]
   realtype a[6];
            ^
c-interface-superpose.cc:233:12: warning: unused variable 'vol' [-Wunused-variable]
   realtype vol;
            ^
c-interface-superpose.cc:234:7: warning: unused variable 'orthcode' [-Wunused-variable]
   int orthcode;
       ^
c-interface-superpose.cc:238:8: warning: unused variable 'success' [-Wunused-variable]
   bool success = coot::util::copy_cell_and_symm_headers(m1, m2);
        ^
c-interface-superpose.cc: In function 'scm_unused_struct* apply_lsq_matches(int, int)':
c-interface-superpose.cc:485:17: warning: variable 'new_cell' set but not used [-Wunused-but-set-variable]
   clipper::Cell new_cell = g.molecules[imol_reference].cell().second;
                 ^
c-interface-superpose.cc: In function 'GtkWidget* wrapped_create_least_squares_dialog()':
c-interface-superpose.cc:620:8: warning: unused variable 'imol_reference' [-Wunused-variable]
    int imol_reference = -1;
        ^
c-interface-superpose.cc:621:8: warning: unused variable 'imol_moving' [-Wunused-variable]
    int imol_moving = -1;
        ^
c-interface-superpose.cc:622:8: warning: unused variable 'ref_start_resno' [-Wunused-variable]
    int ref_start_resno = -9999;
        ^
c-interface-superpose.cc:623:8: warning: unused variable 'ref_end_resno' [-Wunused-variable]
    int ref_end_resno =   -9999;
        ^
c-interface-superpose.cc:624:8: warning: unused variable 'mov_start_resno' [-Wunused-variable]
    int mov_start_resno = -9999;
        ^
c-interface-superpose.cc:625:8: warning: unused variable 'mov_end_resno' [-Wunused-variable]
    int mov_end_resno =   -9999;
        ^
c-interface-superpose.cc:626:8: warning: unused variable 'match_type' [-Wunused-variable]
    int match_type = -1; /* 0: CA
        ^
c-interface-superpose.cc:629:16: warning: unused variable 'ref_chain_id' [-Wunused-variable]
    const char *ref_chain_id = 0;
                ^
c-interface-superpose.cc:630:16: warning: unused variable 'mov_chain_id' [-Wunused-variable]
    const char *mov_chain_id = 0;
                ^
c-interface-superpose.cc:639:15: warning: unused variable 'match_type_all_check_button' [-Wunused-variable]
    GtkWidget *match_type_all_check_button =  lookup_widget(lsq_dialog, "least_squares_match_type_all_radiobutton");
               ^
c-interface-superpose.cc:640:15: warning: unused variable 'match_type_main_check_button' [-Wunused-variable]
    GtkWidget *match_type_main_check_button = lookup_widget(lsq_dialog, "least_squares_match_type_main_radiobutton");
               ^
c-interface-superpose.cc:641:15: warning: unused variable 'match_type_main_calpha_button' [-Wunused-variable]
    GtkWidget *match_type_main_calpha_button =lookup_widget(lsq_dialog, "least_squares_match_type_calpha_radiobutton");
               ^
c-interface-superpose.cc:645:16: warning: unused variable 'txt' [-Wunused-variable]
    const char *txt = 0;
                ^
c-interface-superpose.cc: In function 'int apply_lsq_matches_by_widget(GtkWidget*)':
c-interface-superpose.cc:714:15: warning: unused variable 'mov_option_menu' [-Wunused-variable]
    GtkWidget *mov_option_menu = lookup_widget(lsq_dialog, "least_squares_moving_molecule_optionmenu");
               ^
c-interface-superpose.cc:715:15: warning: unused variable 'ref_option_menu' [-Wunused-variable]
    GtkWidget *ref_option_menu = lookup_widget(lsq_dialog, "least_squares_reference_molecule_optionmenu");
               ^
c-interface-superpose.cc:724:15: warning: unused variable 'ref_mol_chain_id_option_menu' [-Wunused-variable]
    GtkWidget *ref_mol_chain_id_option_menu = lookup_widget(lsq_dialog, "least_squares_reference_chain_id");
               ^
c-interface-superpose.cc:725:15: warning: unused variable 'mov_mol_chain_id_option_menu' [-Wunused-variable]
    GtkWidget *mov_mol_chain_id_option_menu = lookup_widget(lsq_dialog, "least_squares_moving_chain_id");
               ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-waters.o c-interface-waters.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-view.cc:31:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
c-interface-validate.cc: In function 'GtkWidget* wrapped_create_check_waters_dialog()':
c-interface-validate.cc:142:15: warning: unused variable 'menu' [-Wunused-variable]
    GtkWidget *menu = gtk_option_menu_get_menu(GTK_OPTION_MENU(optionmenu));
               ^
c-interface-validate.cc: In function 'void do_check_waters_by_widget(GtkWidget*)':
c-interface-validate.cc:244:15: warning: unused variable 'hbox1' [-Wunused-variable]
    GtkWidget *hbox1 = lookup_widget(dialog, "check_waters_b_factor_hbox");
               ^
c-interface-validate.cc:245:15: warning: unused variable 'hbox2' [-Wunused-variable]
    GtkWidget *hbox2 = lookup_widget(dialog, "check_waters_sigma_level_hbox");
               ^
c-interface-validate.cc:246:15: warning: unused variable 'hbox3' [-Wunused-variable]
    GtkWidget *hbox3 = lookup_widget(dialog, "check_waters_min_dist_hbox");
               ^
c-interface-validate.cc:247:15: warning: unused variable 'hbox4' [-Wunused-variable]
    GtkWidget *hbox4 = lookup_widget(dialog, "check_waters_max_dist_hbox");
               ^
c-interface-validate.cc: In function 'void unset_geometry_graph(GtkWidget*)':
c-interface-validate.cc:597:20: warning: unused variable 'g' [-Wunused-variable]
    graphics_info_t g;
                    ^
c-interface-validate.cc: In function 'void add_on_validation_graph_mol_options(GtkWidget*, const char*)':
c-interface-validate.cc:732:14: warning: variable 'found_validation_type' set but not used [-Wunused-but-set-variable]
    short int found_validation_type = 0;
              ^
c-interface-validate.cc: In function 'void probe_mol_selector_activate(GtkMenuItem*, gpointer)':
c-interface-validate.cc:884:23: warning: unused variable 'g' [-Wunused-variable]
       graphics_info_t g;
                       ^
c-interface-view.cc: In function 'void orient_view(int, const coot::residue_spec_t&, const coot::residue_spec_t&)':
c-interface-view.cc:53:22: warning: variable 'b_to_f_cart' set but not used [-Wunused-but-set-variable]
      coot::Cartesian b_to_f_cart = f - b;
                      ^
c-interface-validate.cc: In function 'void fill_ramachandran_plot_differences_option_menu_with_chain_options(GtkWidget*, int)':
c-interface-validate.cc:1458:15: warning: variable 'mol_optionmenu' set but not used [-Wunused-but-set-variable]
    GtkWidget *mol_optionmenu = NULL;
               ^
c-interface-validate.cc: In function 'void gln_asn_b_factor_outliers(int)':
c-interface-validate.cc:1812:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<v.size(); i++) {
                             ^
c-interface-validate.cc:1818:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<v.size(); i++) {
                             ^
c-interface-validate.cc: In function 'void gln_asn_b_factor_outliers_py(int)':
c-interface-validate.cc:1896:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int i=0; i<v.size(); i++) {
                             ^
c-interface-validate.cc:1902:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int i=0; i<v.size(); i++) {
                                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-waters.cc:49:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-widgets.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-widgets.cc:33:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-waters.cc:53:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
c-interface-widgets.cc: In function 'void remarks_dialog(int)':
c-interface-widgets.cc:122:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i=0; i<l; i++) { 
                               ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-waters-gui.o c-interface-waters-gui.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface.o c-interface.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-waters-gui.cc:49:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from c-interface-waters-gui.cc:53:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o c-interface-test.o c-interface-test.cc
In file included from c-interface-scm.hh:32:0,
                 from c-interface.cc:46:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
c-interface-waters-gui.cc: In function 'void find_waters(int, int, short int, float, short int)':
c-interface-waters-gui.cc:512:15: warning: unused variable 'bf' [-Wunused-variable]
         float bf = graphics_info_t::default_new_atoms_b_factor;
               ^
In file included from c-interface-scm.hh:32:0,
                 from c-interface-test.cc:45:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c callbacks.c
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface.cc:98:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
callbacks.c: In function 'on_ok_button_coordinates_clicked':
callbacks.c:204:16: warning: unused variable 'filename' [-Wunused-variable]
   const gchar *filename; 
                ^
callbacks.c: In function 'on_ok_button_dataset_clicked':
callbacks.c:301:7: warning: unused variable 'itmp' [-Wunused-variable]
   int itmp = -1;
       ^
callbacks.c: In function 'on_about1_activate':
callbacks.c:392:15: warning: unused variable 'text_widget' [-Wunused-variable]
    GtkWidget *text_widget;
               ^
callbacks.c: In function 'on_show_symmetry_ok_button_clicked':
callbacks.c:681:8: warning: unused variable 'imol' [-Wunused-variable]
    int imol = 0;  /* FIXME */
        ^
callbacks.c: In function 'on_show_symmetry_apply_button_clicked':
callbacks.c:770:8: warning: unused variable 'imol' [-Wunused-variable]
    int imol = 0;  /* FIXME */
        ^
callbacks.c: In function 'on_anisotropic_atoms1_activate':
callbacks.c:885:8: warning: unused variable 'imol' [-Wunused-variable]
    int imol = 0;  /* FIXME */
        ^
callbacks.c: In function 'on_show_aniso_ok_button_clicked':
callbacks.c:948:8: warning: unused variable 'imol' [-Wunused-variable]
    int imol = 0; /* FIXME */
        ^
callbacks.c: In function 'on_go_to_atom_cancel_button_clicked':
callbacks.c:1457:14: warning: variable 'optionmenu' set but not used [-Wunused-but-set-variable]
   GtkWidget *optionmenu; 
              ^
callbacks.c: In function 'on_find_ligand_many_atoms_continue_button_clicked':
callbacks.c:2078:4: warning: implicit declaration of function 'execute_ligand_search' [-Wimplicit-function-declaration]
    execute_ligand_search();
    ^
callbacks.c: In function 'on_save_coords_dialog_save_button_clicked':
callbacks.c:2181:14: warning: variable 'active_menu' set but not used [-Wunused-but-set-variable]
   GtkWidget *active_menu;
              ^
callbacks.c: In function 'on_pointer_atom_type_ok_button_clicked':
callbacks.c:3807:9: warning: unused variable 'type' [-Wunused-variable]
   char *type;
         ^
callbacks.c: In function 'on_run_refmac_phase_input_optionmenu_changed':
callbacks.c:3976:14: warning: unused variable 'sad_checkbutton' [-Wunused-variable]
   GtkWidget *sad_checkbutton;
              ^
callbacks.c: In function 'on_run_refmac_twin_checkbutton_toggled':
callbacks.c:4057:14: warning: unused variable 'mtz_file_frame' [-Wunused-variable]
   GtkWidget *mtz_file_frame  = lookup_widget(GTK_WIDGET(togglebutton), "run_refmac_mtz_file_hbox");
              ^
callbacks.c: In function 'on_run_refmac_mtz_filechooser_button_clicked':
callbacks.c:4212:16: warning: unused variable 'mtz_filename' [-Wunused-variable]
   const gchar *mtz_filename;
                ^
callbacks.c:4211:14: warning: unused variable 'mtz_file_label' [-Wunused-variable]
   GtkWidget *mtz_file_label;
              ^
callbacks.c: In function 'on_centre_atom_label_ok_button_clicked':
callbacks.c:5412:14: warning: unused variable 'off' [-Wunused-variable]
   GtkWidget *off = lookup_widget(dialog, "centre_atom_label_radiobutton_off");
              ^
callbacks.c: In function 'on_column_label_expert_mode_button_clicked':
callbacks.c:5651:13: warning: unused variable 'is_expert_mode_flag' [-Wunused-variable]
   short int is_expert_mode_flag; 
             ^
callbacks.c: In function 'on_preferences_destroy':
callbacks.c:6489:14: warning: unused variable 'w' [-Wunused-variable]
   GtkWidget *w = lookup_widget(GTK_WIDGET(object), "preferences");
              ^
callbacks.c: In function 'on_preferences_model_toolbar_right_radiobutton_toggled':
callbacks.c:7669:14: warning: unused variable 'show' [-Wunused-variable]
   GtkWidget *show = lookup_widget(GTK_WIDGET(togglebutton), "preferences_model_toolbar_show_radiobutton");
              ^
callbacks.c: In function 'on_preferences_model_toolbar_left_radiobutton_toggled':
callbacks.c:7683:14: warning: unused variable 'show' [-Wunused-variable]
   GtkWidget *show = lookup_widget(GTK_WIDGET(togglebutton), "preferences_model_toolbar_show_radiobutton");
              ^
callbacks.c: In function 'on_preferences_model_toolbar_top_radiobutton_toggled':
callbacks.c:7697:14: warning: unused variable 'show' [-Wunused-variable]
   GtkWidget *show = lookup_widget(GTK_WIDGET(togglebutton), "preferences_model_toolbar_show_radiobutton");
              ^
callbacks.c: In function 'on_preferences_model_toolbar_bottom_radiobutton_toggled':
callbacks.c:7711:14: warning: unused variable 'show' [-Wunused-variable]
   GtkWidget *show = lookup_widget(GTK_WIDGET(togglebutton), "preferences_model_toolbar_show_radiobutton");
              ^
callbacks.c: In function 'on_pointer_distances_checkbutton_toggled':
callbacks.c:8060:15: warning: unused variable 'dialog' [-Wunused-variable]
    GtkWidget *dialog = lookup_widget(GTK_WIDGET(togglebutton), "pointer_distances_dialog");
               ^
callbacks.c: In function 'on_delete_item_dialog_destroy':
callbacks.c:8245:15: warning: unused variable 'w' [-Wunused-variable]
    GtkWidget *w = GTK_WIDGET(object);
               ^
callbacks.c: In function 'on_ncs_controller_molecule_n_display_chain_ich_checkbutton_toggled':
callbacks.c:9037:15: warning: unused variable 'w' [-Wunused-variable]
    GtkWidget *w = lookup_widget(GTK_WIDGET(togglebutton), "ncs_control_dialog"); 
               ^
callbacks.c: In function 'on_dataset_filechooserdialog1_response':
callbacks.c:10647:7: warning: unused variable 'itmp' [-Wunused-variable]
   int itmp = -1;
       ^
callbacks.c: In function 'on_refine_params_weight_matrix_entry_changed':
callbacks.c:11974:16: warning: unused variable 'text' [-Wunused-variable]
   const gchar *text = gtk_entry_get_text(GTK_ENTRY(entry));
                ^
callbacks.c: In function 'on_multi_residue_torsion_cancel_button_clicked':
callbacks.c:12052:3: warning: implicit declaration of function 'clear_multi_residue_torsion_mode' [-Wimplicit-function-declaration]
   clear_multi_residue_torsion_mode();
   ^
callbacks.c: In function 'on_multi_residue_torsion_reverse_checkbutton_toggled':
callbacks.c:12077:5: warning: implicit declaration of function 'set_multi_residue_torsion_reverse_mode' [-Wimplicit-function-declaration]
     set_multi_residue_torsion_reverse_mode(1);
     ^
callbacks.c: In function 'on_multi_residue_torsion_pick_apply_button_clicked':
callbacks.c:12095:3: warning: implicit declaration of function 'show_multi_residue_torsion_dialog' [-Wimplicit-function-declaration]
   show_multi_residue_torsion_dialog();
   ^
callbacks.c: In function 'on_multi_residue_torsion_start_button_clicked':
callbacks.c:12128:3: warning: implicit declaration of function 'setup_multi_residue_torsion' [-Wimplicit-function-declaration]
   setup_multi_residue_torsion(); // shows a dialog
   ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o cmtz-interface.o cmtz-interface.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from c-interface-test.cc:95:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from c-interface-test.cc:140:0:
../goograph/goograph.hh: In member function 'bool coot::goograph::is_valid_trace(int)':
../goograph/goograph.hh:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (trace_id >= traces.size()) {
                                  ^
c-interface-test.cc: In function 'int test_function(int, int)':
c-interface-test.cc:169:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iround=0; iround<n_rounds; iround++) { 
                                         ^
c-interface-test.cc:244:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i<l; i++) { 
                            ^
c-interface.cc: In function 'int handle_read_draw_molecule_with_recentre(const char*, int)':
c-interface.cc:527:10: warning: unused variable 'n_bonds' [-Wunused-variable]
      int n_bonds = g.Geom_p()->try_dynamic_add(types_with_no_dictionary[i],
          ^
c-interface-test.cc: In function 'scm_unused_struct* test_function_scm(SCM, SCM)':
c-interface-test.cc:398:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int irest=0; irest<g.Geom_p()->size(); irest++) { 
                                                         ^
c-interface-test.cc:428:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iround=0; iround<n_rounds; iround++) {
                                         ^
c-interface-test.cc: In function 'PyObject* test_function_py(PyObject*, PyObject*)':
c-interface-test.cc:482:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
          for (unsigned int iround=0; iround<n_rounds; iround++) {
                                             ^
c-interface.cc: In function 'scm_unused_struct* additional_representation_info_scm(int)':
c-interface.cc:2555:72: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int ir=0; ir<graphics_info_t::molecules[imol].add_reps.size(); ir++) {
                                                                        ^
c-interface.cc: In function 'PyObject* additional_representation_info_py(int)':
c-interface.cc:2602:72: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int ir=0; ir<graphics_info_t::molecules[imol].add_reps.size(); ir++) {
                                                                        ^
c-interface.cc: In function 'gchar* get_text_for_phs_cell_chooser(int, char*)':
c-interface.cc:3978:25: warning: variable 'ccell' set but not used [-Wunused-but-set-variable]
     clipper::Cell       ccell      = g.molecules[imol].xmap_list[0].cell();
                         ^
c-interface.cc: In function 'void display_maps_scm(SCM)':
c-interface.cc:4753:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) {
                                ^
c-interface.cc:4764:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imol=0; imol<n_mol; imol++) { 
                                   ^
c-interface.cc: In function 'void display_maps_py(PyObject*)':
c-interface.cc:4785:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n; i++) {
                                ^
c-interface.cc:4795:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imol=0; imol<n_mol; imol++) { 
                                   ^
c-interface.cc: In function 'PyObject* py_clean_internal(PyObject*)':
c-interface.cc:5228:7: warning: unused variable 'i' [-Wunused-variable]
   int i = PyInt_AsLong(o);
       ^
c-interface.cc:5233:10: warning: unused variable 'i' [-Wunused-variable]
      int i=PyInt_AsLong(o);
          ^
c-interface.cc: In function 'int handle_shelx_fcf_file_internal(const char*)':
c-interface.cc:6472:20: warning: unused variable 'g' [-Wunused-variable]
    graphics_info_t g;
                    ^
c-interface.cc: In function 'void remove_this_view()':
c-interface.cc:7334:8: warning: variable 'r' set but not used [-Wunused-but-set-variable]
    int r=0;
        ^
c-interface.cc: In function 'int go_to_view_number(int, int)':
c-interface.cc:7378:7: warning: variable 'nsteps' set but not used [-Wunused-but-set-variable]
   int nsteps = 2000;
       ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from cmtz-interface.cc:58:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from cmtz-interface.cc:58:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o command-line.o command-line.cc
cmtz-interface.cc: In function 'void coot::setup_refmac_parameters(GtkWidget*, const coot::mtz_column_types_info_t&)':
cmtz-interface.cc:186:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (i=0; i<col_labs.f_cols.size(); i++) { 
                                     ^
cmtz-interface.cc:194:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (i=0; i<col_labs.sigf_cols.size(); i++) {
                                        ^
cmtz-interface.cc:212:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.r_free_cols.size(); i++) {
                                         ^
cmtz-interface.cc: In function 'void coot::setup_refmac_parameters_from_file(GtkWidget*)':
cmtz-interface.cc:361:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.f_cols.size(); i++) {
                                    ^
cmtz-interface.cc:364:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j<col_labs.sigf_cols.size(); j++) {
                                              ^
cmtz-interface.cc:402:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.fpm_cols.size(); i++) {
                                      ^
cmtz-interface.cc:404:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (i+1 < col_labs.fpm_cols.size()) {
                                       ^
cmtz-interface.cc:407:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int j=0; j<col_labs.sigfpm_cols.size(); j++) {
                                                  ^
cmtz-interface.cc:409:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (j+1 < col_labs.sigfpm_cols.size()) {
                                       ^
cmtz-interface.cc:445:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.i_cols.size(); i++) {
                                    ^
cmtz-interface.cc:448:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int j=0; j<col_labs.sigf_cols.size(); j++) {
                                              ^
cmtz-interface.cc:482:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.ipm_cols.size(); i++) {
                                      ^
cmtz-interface.cc:484:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (i+1 < col_labs.ipm_cols.size()) {
                                       ^
cmtz-interface.cc:487:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (int j=0; j<col_labs.sigipm_cols.size(); j++) {
                                                  ^
cmtz-interface.cc:489:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (j+1 < col_labs.sigipm_cols.size()) {
                                       ^
cmtz-interface.cc:526:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (i=0; i<col_labs.r_free_cols.size(); i++) {
                                          ^
cmtz-interface.cc:535:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.phi_cols.size(); i++) {
                                      ^
cmtz-interface.cc:543:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.weight_cols.size(); i++) {
                                         ^
cmtz-interface.cc:558:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i<col_labs.hl_cols.size(); i++) {
                                     ^
cmtz-interface.cc:563:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (i+1 < col_labs.hl_cols.size()) {
                                     ^
cmtz-interface.cc: In function 'void refmac_dialog_f_button_select(GtkWidget*, GtkPositionType)':
cmtz-interface.cc:777:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<save_f_phi_columns->sigf_cols.size(); i++) {
                                                      ^
cmtz-interface.cc: In function 'void refmac_dialog_fpm_button_select(GtkWidget*, GtkPositionType)':
cmtz-interface.cc:810:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<save_f_phi_columns->sigfpm_cols.size()-1; i++) {
                                                          ^
cmtz-interface.cc: In function 'void refmac_dialog_i_button_select(GtkWidget*, GtkPositionType)':
cmtz-interface.cc:833:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<save_f_phi_columns->sigf_cols.size(); i++) {
                                                      ^
cmtz-interface.cc: In function 'void refmac_dialog_ipm_button_select(GtkWidget*, GtkPositionType)':
cmtz-interface.cc:856:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<save_f_phi_columns->sigipm_cols.size()-1; i++) {
                                                          ^
cmtz-interface.cc: In function 'void coot::fill_f_optionmenu(GtkWidget*, short int)':
cmtz-interface.cc:940:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i=0; i< save_f_phi_columns->f_cols.size(); i++) {
                                                    ^
cmtz-interface.cc:964:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0; i< save_f_phi_columns->d_cols.size(); i++) { 
                                                ^
cmtz-interface.cc: In function 'GtkWidget* coot::column_selector_using_cmtz(const string&)':
cmtz-interface.cc:1058:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (i=0; i< f_phi_columns->phi_cols.size(); i++) {
                                              ^
cmtz-interface.cc:1087:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (i=0; i< f_phi_columns->weight_cols.size(); i++) {
                                                 ^
cmtz-interface.cc:992:8: warning: variable 'is_cif' set but not used [-Wunused-but-set-variable]
    int is_cif = 0;
        ^
cmtz-interface.cc:993:8: warning: unused variable 'is_cns_data' [-Wunused-variable]
    int is_cns_data = 0;
        ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from command-line.cc:59:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from command-line.cc:59:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-colour.o coot-colour.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-align.o coot-align.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-nomenclature.o coot-nomenclature.cc
command-line.cc: In member function 'void command_line_data::roberto_pdbs(int, char**)':
command-line.cc:491:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=1; i<argc; i++) {
                             ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from coot-align.cc:10:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from coot-align.hh:2:0,
                 from coot-align.cc:11:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
coot-align.cc: In member function 'void coot::chain_mutation_info_container_t::rationalize_insertions()':
coot-align.cc:48:11: warning: variable 'running_end' set but not used [-Wunused-but-set-variable]
       int running_end = 0;
           ^
In file included from ../ideal/simple-restraint.hh:163:0,
                 from coot-nomenclature.cc:25:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from ../ligand/richardson-rotamer.hh:25,
                 from coot-nomenclature.cc:31:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c coot-glue.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c coot-glue-gtk2.c
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot-hydrogens.o coot-hydrogens.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot_pythonmodule.o coot_pythonmodule.cc
swig -o coot_wrap_guile_pre_gtk1.cc -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_LIBCURL -I../src -guile -c++ ../src/coot.i
swig -o coot_wrap_guile_pre_gtk2.cc -DCOOT_USE_GTK2_INTERFACE  -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -DUSE_LIBCURL -I../src -guile -c++  ../src/coot.i
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o drag-and-drop.o drag-and-drop.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o geometry-graphs.o geometry-graphs.cc
In file included from cc-interface.hh:28:0,
                 from drag-and-drop.cc:15:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from geometry-graphs.cc:26:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o get-residue.o get-residue.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o flev.o flev.cc
geometry-graphs.cc: In member function 'void coot::geometry_graphs::render_geometry_distortion_blocks_internal(const coot::geometry_distortion_info_container_t&)':
geometry-graphs.cc:239:29: warning: unused variable 'idx_4' [-Wunused-variable]
    int idx_1, idx_2, idx_3, idx_4;
                             ^
geometry-graphs.cc:240:27: warning: variable 'occ_3' set but not used [-Wunused-but-set-variable]
    realtype occ_1, occ_2, occ_3;
                           ^
geometry-graphs.cc: In member function 'void coot::geometry_graphs::render_b_factor_blocks(int, int, const string&, int, const std::vector<coot::b_factor_block_info_t>&)':
geometry-graphs.cc:618:8: warning: variable 'this_resno' set but not used [-Wunused-but-set-variable]
    int this_resno;
        ^
geometry-graphs.cc: In member function 'void coot::geometry_graphs::update_omega_blocks(const coot::omega_distortion_info_container_t&, int, const string&)':
geometry-graphs.cc:775:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   offsetted_residue_number < blocks[chain_index].size()) { 
                                                       ^
geometry-graphs.cc: In member function 'void coot::geometry_graphs::draw_chain_axis(int, int) const':
geometry-graphs.cc:1049:19: warning: variable 'item' set but not used [-Wunused-but-set-variable]
    GtkCanvasItem *item;
                   ^
geometry-graphs.cc: In member function 'void coot::geometry_graphs::draw_chain_axis_tick_and_tick_labels(int, int, int) const':
geometry-graphs.cc:1077:19: warning: variable 'item' set but not used [-Wunused-but-set-variable]
    GtkCanvasItem *item;
                   ^
geometry-graphs.cc: In member function 'void coot::geometry_graphs::label_chain(const string&, int) const':
geometry-graphs.cc:1132:19: warning: variable 'item' set but not used [-Wunused-but-set-variable]
    GtkCanvasItem *item;
                   ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o generic-objects.o generic-objects.cc
In file included from ../lbg/lbg.hh:53:0,
                 from flev.cc:31:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from cc-interface.hh:28:0,
                 from generic-objects.cc:35:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lbg/lbg.hh:61:0,
                 from flev.cc:31:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from get-residue.cc:7:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from get-residue.cc:7:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from generic-objects.cc:36:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o globjects.o globjects.cc
flev.cc: In function 'bool flev_check_for_hydrogens(CResidue*, const std::vector<CResidue*>&, coot::protein_geometry*)':
flev.cc:96:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_residue_atoms; i++) { 
                             ^
flev.cc:106:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                    ^
flev.cc: In function 'void coot::write_fle_centres(const std::vector<coot::fle_residues_helper_t>&, const std::vector<coot::fle_ligand_bond_t>&, const std::vector<coot::solvent_exposure_difference_helper_t>&, const coot::pi_stacking_container_t&, CResidue*)':
flev.cc:1367:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                  ^
flev.cc: In function 'void coot::write_ligand_atom_accessibilities(const std::vector<std::pair<coot::atom_spec_t, float> >&, const coot::flev_attached_hydrogens_t&, CResidue*)':
flev.cc:1486:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++) {
                                ^
flev.cc: In function 'std::vector<coot::fle_ligand_bond_t> coot::get_metal_bonds(CResidue*, const std::vector<CResidue*>&)':
flev.cc:1894:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int irat=0; irat<n_residue_atoms; irat++) {
                                  ^
flev.cc:1895:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int ilat=0; ilat<n_residue_atoms; ilat++) {
                                     ^
flev.cc: In function 'bool coot::is_a_metal(CResidue*)':
flev.cc:1932:9: warning: unused variable 'r' [-Wunused-variable]
    bool r = 0;
         ^
flev.cc: In function 'double coot::find_water_protein_length(CResidue*, CMMDBManager*)':
flev.cc:2001:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int il=0; il<n_ligand_residue_atoms; il++) {
                                    ^
flev.cc:2002:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int irat=0; irat<n_residue_atoms; irat++) {
                                    ^
flev.cc: In member function 'void coot::flev_attached_hydrogens_t::distances_to_protein(CResidue*, CMMDBManager*)':
flev.cc:2620:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int itor=0; itor<n_torsion_samples; itor++) {
                                     ^
flev.cc: In member function 'void coot::flev_attached_hydrogens_t::distances_to_protein_using_correct_Hs(CResidue*, CMMDBManager*, const coot::protein_geometry&)':
flev.cc:2674:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_ligand_atoms; iat++) { 
                                    ^
flev.cc:2704:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_ligand_atoms; iat++) { 
                                    ^
flev.cc:2728:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int itor=0; itor<n_torsion_samples; itor++) {
                                     ^
flev.cc: In member function 'std::pair<clipper::Coord_orth, clipper::Coord_orth> coot::flev_attached_hydrogens_t::hydrogen_pos(const coot::named_torsion_t&, CResidue*) const':
flev.cc:2766:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_residue_atoms; i++) {
                             ^
flev.cc: In member function 'clipper::Coord_orth coot::flev_attached_hydrogens_t::get_atom_pos_bonded_to_atom(CAtom*, CAtom*, CResidue*, const coot::protein_geometry&) const':
flev.cc:2843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<n_residue_atoms ; iat++) {
                                ^
flev.cc: In member function 'std::vector<CAtom*> coot::flev_attached_hydrogens_t::close_atoms(const clipper::Coord_orth&, const std::vector<CResidue*>&) const':
flev.cc:2884:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
flev.cc: In member function 'coot::bash_distance_t coot::flev_attached_hydrogens_t::find_bash_distance(const clipper::Coord_orth&, const clipper::Coord_orth&, const std::vector<CAtom*>&) const':
flev.cc:2920:11: warning: unused variable 'max_dist_squared' [-Wunused-variable]
    double max_dist_squared = max_dist * max_dist;
           ^
generic-objects.cc: In function 'void to_generic_object_add_dashed_line(int, const char*, int, float, float, float, float, float, float, float)':
generic-objects.cc:96:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int idash=0; idash<(n_dashes-1); idash++) {
                                                ^
generic-objects.cc: In function 'void to_generic_object_add_point(int, const char*, int, float, float, float)':
generic-objects.cc:130:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (object_number >=0 && object_number < g.generic_objects_p->size()) { 
                                                                       ^
generic-objects.cc: In function 'void to_generic_object_add_arc(int, const char*, int, float, float, float, float, float, float, float, float, float, float, float)':
generic-objects.cc:159:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (object_number >=0 && object_number < g.generic_objects_p->size()) {
                                                                       ^
generic-objects.cc: In function 'void to_generic_object_add_display_list_handle(int, int)':
generic-objects.cc:187:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (object_number >=0 && object_number < g.generic_objects_p->size()) { 
                                                                       ^
generic-objects.cc: In function 'void set_display_generic_object(int, short int)':
generic-objects.cc:201:72: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (object_number >=0  && object_number < g.generic_objects_p->size()) {
                                                                        ^
generic-objects.cc: In function 'int generic_object_is_displayed_p(int)':
generic-objects.cc:217:72: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (object_number >=0  && object_number < g.generic_objects_p->size()) {
                                                                        ^
generic-objects.cc: In function 'void handle_read_draw_probe_dots(const char*)':
generic-objects.cc:357:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i< nobjs; i++) {
                             ^
generic-objects.cc:389:13: warning: unused variable 'n_bits' [-Wunused-variable]
         int n_bits = 3;
             ^
generic-objects.cc: In function 'void handle_read_draw_probe_dots_unformatted(const char*, int, int)':
generic-objects.cc:459:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i< nobjs; i++) {
                             ^
generic-objects.cc:480:8: warning: variable 'contact_type2' set but not used [-Wunused-but-set-variable]
   char contact_type2[3];
        ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from globjects.cc:74:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from globjects.cc:81:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
globjects.cc: In function 'GtkWidget* gl_extras(GtkWidget*, short int)':
globjects.cc:1264:20: warning: unused variable 'g' [-Wunused-variable]
    graphics_info_t g;
                    ^
globjects.cc: In function 'gint draw_mono(GtkWidget*, GdkEventExpose*, short int)':
globjects.cc:2042:19: warning: variable 'fbs' set but not used [-Wunused-but-set-variable]
   coot::Cartesian fbs = front_to_back.by_scalar(-0.2);
                   ^
globjects.cc: In function 'gint key_press_event(GtkWidget*, GdkEventKey*)':
globjects.cc:3050:7: warning: unused variable 'rot_trans_rotation_origin_atom' [-Wunused-variable]
   int rot_trans_rotation_origin_atom = 0; // flag for Ctrl left
       ^
globjects.cc:3385:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (event->keyval == graphics_info_t::ncs_next_chain_skip_key) {
                                             ^
globjects.cc:3400:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (event->keyval == graphics_info_t::ncs_prev_chain_skip_key) {
                                             ^
globjects.cc:3416:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (event->keyval == graphics_info_t::update_go_to_atom_from_current_residue_key) {
                                             ^
globjects.cc: In function 'gint glarea_button_press(GtkWidget*, GdkEventButton*)':
globjects.cc:3953:20: warning: unused variable 'my_button3_mask' [-Wunused-variable]
    GdkModifierType my_button3_mask = info.gdk_button3_mask();
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info.o graphics-info.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-defines.o graphics-info-defines.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-defines.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-defines.cc:33:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info.cc:55:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from graphics-info.cc:68:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
graphics-info.cc: In member function 'void graphics_info_t::smooth_scroll_maybe_sinusoidal_acceleration(float, float, float, short int, float)':
graphics-info.cc:688:13: warning: unused variable 'stepping_x' [-Wunused-variable]
       float stepping_x = frac*xd;
             ^
graphics-info.cc:689:13: warning: unused variable 'stepping_y' [-Wunused-variable]
       float stepping_y = frac*yd;
             ^
graphics-info.cc:690:13: warning: unused variable 'stepping_z' [-Wunused-variable]
       float stepping_z = frac*zd;
             ^
graphics-info.cc: In member function 'void graphics_info_t::environment_graphics_object_internal_tubes(const graphical_bonds_container&) const':
graphics-info.cc:1772:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int ipart=0; ipart<n_parts; ipart++) {
                                      ^
graphics-info.cc: In member function 'void graphics_info_t::graphics_object_internal_torus(const coot::Cartesian&, const coot::Cartesian&, const double&, const double&, int) const':
graphics-info.cc:1955:11: warning: unused variable 'top' [-Wunused-variable]
    double top =  0.2;
           ^
graphics-info.cc:1956:11: warning: unused variable 'base' [-Wunused-variable]
    double base = 0.2;
           ^
graphics-info.cc:1957:11: warning: unused variable 'fraction_head_size' [-Wunused-variable]
    double fraction_head_size = 0.3;
           ^
graphics-info.cc:1958:8: warning: unused variable 'slices' [-Wunused-variable]
    int slices  = 12;
        ^
graphics-info.cc:1959:8: warning: unused variable 'stacks' [-Wunused-variable]
    int stacks  = 2;
        ^
graphics-info.cc: In member function 'double graphics_info_t::get_geometry_torsion() const':
graphics-info.cc:2370:24: warning: variable 'v3r' set but not used [-Wunused-but-set-variable]
    clipper::Coord_orth v3r = p4 - p3;
                        ^
graphics-info.cc: In member function 'int graphics_info_t::Imol_Refinement_Map() const':
graphics-info.cc:2476:8: warning: unused variable 'only_map' [-Wunused-variable]
    int only_map = -1;  // gets set, maybe (when not a difference map)
        ^
graphics-info.cc: In member function 'void graphics_info_t::setup_flash_bond_internal(int)':
graphics-info.cc:3776:78: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        if (i_torsion_index >= 0 && i_torsion_index < torsion_restraints.size()) {
                                                                              ^
graphics-info.cc:3765:10: warning: unused variable 'add_reverse_contacts' [-Wunused-variable]
     bool add_reverse_contacts = 0;
          ^
graphics-info.cc: In static member function 'static void graphics_info_t::draw_generic_objects_solid()':
graphics-info.cc:4316:88: warning: narrowing conversion of '(((double)graphics_info_t::generic_objects_p->std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_object_t, std::allocator<coot::generic_display_object_t> >(i).coot::generic_display_object_t::lines_set.std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_line_set_t, std::allocator<coot::generic_display_line_set_t> >(ils).coot::generic_display_line_set_t::colour.coot::colour_holder::red) * 8.0000000000000004e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
         GLfloat  mat_diffuse[]  = {(*generic_objects_p)[i].lines_set[ils].colour.red   * 0.8,
                                                                                        ^
graphics-info.cc:4317:60: warning: narrowing conversion of '(((double)graphics_info_t::generic_objects_p->std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_object_t, std::allocator<coot::generic_display_object_t> >(i).coot::generic_display_object_t::lines_set.std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_line_set_t, std::allocator<coot::generic_display_line_set_t> >(ils).coot::generic_display_line_set_t::colour.coot::colour_holder::green) * 8.0000000000000004e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
        (*generic_objects_p)[i].lines_set[ils].colour.green * 0.8,
                                                            ^
graphics-info.cc:4318:60: warning: narrowing conversion of '(((double)graphics_info_t::generic_objects_p->std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_object_t, std::allocator<coot::generic_display_object_t> >(i).coot::generic_display_object_t::lines_set.std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_line_set_t, std::allocator<coot::generic_display_line_set_t> >(ils).coot::generic_display_line_set_t::colour.coot::colour_holder::blue) * 8.0000000000000004e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
        (*generic_objects_p)[i].lines_set[ils].colour.blue  * 0.8, 
                                                            ^
graphics-info.cc:4460:58: warning: narrowing conversion of '(((double)obj.coot::generic_display_object_t::arcs.std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_object_t::arc_t, std::allocator<coot::generic_display_object_t::arc_t> >(iarc).coot::generic_display_object_t::arc_t::col.coot::colour_t::col.std::vector<_Tp, _Alloc>::operator[]<float, std::allocator<float> >(0u)) * 8.0000000000000004e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
     GLfloat  mat_diffuse[]  = {obj.arcs[iarc].col.col[0] * 0.8,
                                                          ^
graphics-info.cc:4461:37: warning: narrowing conversion of '(((double)obj.coot::generic_display_object_t::arcs.std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_object_t::arc_t, std::allocator<coot::generic_display_object_t::arc_t> >(iarc).coot::generic_display_object_t::arc_t::col.coot::colour_t::col.std::vector<_Tp, _Alloc>::operator[]<float, std::allocator<float> >(1u)) * 8.0000000000000004e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
           obj.arcs[iarc].col.col[1] * 0.8,
                                     ^
graphics-info.cc:4462:37: warning: narrowing conversion of '(((double)obj.coot::generic_display_object_t::arcs.std::vector<_Tp, _Alloc>::operator[]<coot::generic_display_object_t::arc_t, std::allocator<coot::generic_display_object_t::arc_t> >(iarc).coot::generic_display_object_t::arc_t::col.coot::colour_t::col.std::vector<_Tp, _Alloc>::operator[]<float, std::allocator<float> >(2u)) * 8.0000000000000004e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
           obj.arcs[iarc].col.col[2] * 0.8, 
                                     ^
graphics-info.cc: In member function 'void graphics_info_t::run_user_defined_click_func()':
graphics-info.cc:5029:11: warning: unused variable 'v' [-Wunused-variable]
       SCM v = scm_apply_1(user_defined_click_scm_func, arg_list, rest);
           ^
graphics-info.cc: In static member function 'static coot::view_info_t coot::view_info_t::interpolate(const coot::view_info_t&, const coot::view_info_t&, int)':
graphics-info.cc:5311:10: warning: variable 'frac_zoom_by' set but not used [-Wunused-but-set-variable]
    float frac_zoom_by =  1;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-graphs.o graphics-info-graphs.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-graphs.cc:45:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from graphics-info-graphs.cc:57:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-gui.o graphics-info-gui.cc
graphics-info-graphs.cc: In function 'GtkWidget* coot::get_validation_graph(int, coot::geometry_graph_type)':
graphics-info-graphs.cc:146:12: warning: variable 'found' set but not used [-Wunused-but-set-variable]
       bool found = 0; 
            ^
graphics-info-graphs.cc: In member function 'void graphics_info_t::delete_residue_from_geometry_graphs(int, coot::residue_spec_t)':
graphics-info-graphs.cc:334:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int igt=0; igt<graph_types.size(); igt++) { 
                                         ^
graphics-info-graphs.cc: In member function 'std::vector<coot::geometry_graph_block_info_generic> graphics_info_t::ncs_diffs_from_mol(int)':
graphics-info-graphs.cc:1390:11: warning: unused variable 'model_p' [-Wunused-variable]
   CModel *model_p = mol->GetModel(imodel);
           ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-modelling.o graphics-info-modelling.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-modelling.cc:61:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from ../ligand/richardson-rotamer.hh:25,
                 from graphics-info-modelling.cc:69:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-gui.cc:58:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
graphics-info-modelling.cc: In member function 'coot::refinement_results_t graphics_info_t::copy_mol_and_refine(int, int, int, std::string, int, std::string, std::string, std::string)':
graphics-info-modelling.cc:148:14: warning: unused variable 'irest' [-Wunused-variable]
    short int irest = 0; // make 1 when restraints found.
              ^
graphics-info-modelling.cc:161:14: warning: unused variable 'have_disulfide_residues' [-Wunused-variable]
    short int have_disulfide_residues = 0;  // other residues are included in the
              ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from graphics-info-gui.cc:71:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
graphics-info-modelling.cc: In member function 'std::pair<int, std::vector<std::basic_string<char> > > graphics_info_t::check_dictionary_for_residue_restraints(CResidue**, int)':
graphics-info-modelling.cc:825:8: warning: unused variable 'status' [-Wunused-variable]
    int status;
        ^
graphics-info-modelling.cc: In member function 'std::pair<CMMDBManager*, std::vector<CResidue*> > graphics_info_t::create_mmdbmanager_from_res_vector(const std::vector<CResidue*>&, int, CMMDBManager*, std::string)':
graphics-info-modelling.cc:984:15: warning: unused variable 'chain_p' [-Wunused-variable]
       CChain *chain_p = new CChain;
               ^
graphics-info-modelling.cc: In member function 'PyObject* graphics_info_t::refinement_results_to_py(coot::refinement_results_t&)':
graphics-info-modelling.cc:1315:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int il=0; il<rr.lights.size(); il++) {
                                        ^
graphics-info-modelling.cc: In member function 'void graphics_info_t::execute_add_terminal_residue(int, const string&, const CResidue*, const string&, const string&, short int)':
graphics-info-modelling.cc:2231:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int i=0; i<tmp_asc.n_selected_atoms; i++) {
                                         ^
graphics-info-modelling.cc:2159:15: warning: variable 'bf' set but not used [-Wunused-but-set-variable]
         float bf = default_new_atoms_b_factor;
               ^
graphics-info-modelling.cc: In member function 'void graphics_info_t::execute_db_main(int, std::string, int, int, std::string)':
graphics-info-modelling.cc:2985:9: warning: unused variable 'bf' [-Wunused-variable]
   float bf = default_new_atoms_b_factor;
         ^
graphics-info-modelling.cc:2912:8: warning: variable 'idbfrags' set but not used [-Wunused-but-set-variable]
    int idbfrags = 0;
        ^
graphics-info-modelling.cc: In member function 'short int graphics_info_t::generate_moving_atoms_from_rotamer(int)':
graphics-info-modelling.cc:3307:10: warning: variable 'i_add' set but not used [-Wunused-but-set-variable]
      int i_add;
          ^
graphics-info-modelling.cc: In member function 'std::pair<std::basic_string<char>, std::basic_string<char> > graphics_info_t::get_chi_atom_names(CResidue*, const coot::dictionary_residue_restraints_t&, int) const':
graphics-info-modelling.cc:3527:72: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ((torsion_index >=0) && (torsion_index < torsion_restraints.size())) {
                                                                        ^
graphics-info-modelling.cc: In member function 'void graphics_info_t::rotate_chi_torsion_general(double, double)':
graphics-info-modelling.cc:3616:14: warning: unused variable 'istat' [-Wunused-variable]
    short int istat = 1; // failure
              ^
graphics-info-modelling.cc: In member function 'void graphics_info_t::rotate_multi_residue_torsion(double, double)':
graphics-info-modelling.cc:3656:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<moving_atoms_asc->n_selected_atoms; i++) {
                                                  ^
graphics-info-gui.cc: In static member function 'static void graphics_info_t::activate_scroll_radio_button_in_display_manager(int)':
graphics-info-gui.cc:779:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i == g.scroll_wheel_map) {
                    ^
graphics-info-gui.cc: In member function 'void graphics_info_t::fill_option_menu_with_coordinates_options_internal_3(GtkWidget*, GtkSignalFunc, std::vector<int>, short int, int)':
graphics-info-gui.cc:1847:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int idx=0; idx<fill_with_these_molecules.size(); idx++) {
                                                          ^
graphics-info-gui.cc:1854:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int idx=0; idx<fill_with_these_molecules.size(); idx++) {
                                                       ^
graphics-info-gui.cc: In member function 'void graphics_info_t::fill_option_menu_with_undo_options(GtkWidget*)':
graphics-info-gui.cc:1952:8: warning: unused variable 'active_mol_no' [-Wunused-variable]
    int active_mol_no = -1;
        ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-navigation.o graphics-info-navigation.cc
graphics-info-gui.cc: In static member function 'static void graphics_info_t::on_multi_residue_torsion_button_clicked(GtkButton*, gpointer)':
graphics-info-gui.cc:3919:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i=0; i<g.moving_atoms_asc->n_selected_atoms; i++) { 
                                                   ^
graphics-info-gui.cc:3905:8: warning: unused variable 'i' [-Wunused-variable]
    int i = GPOINTER_TO_INT(user_data);
        ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk1.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-navigation.cc:50:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-navigation-gtk2.o graphics-info-navigation-gtk2.cc
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-navigation.cc:57:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-navigation-gtk2.cc:42:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-navigation-gtk2.cc:42:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-preferences.o graphics-info-preferences.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-network.o graphics-info-network.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-mutate.o graphics-info-mutate.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-lsq.o graphics-info-lsq.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-network.cc:6:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-network.cc:6:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-preferences.cc:33:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-preferences.cc:33:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-mutate.cc:51:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from graphics-info-mutate.cc:62:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-lsq.cc:46:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from graphics-info-lsq.cc:51:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
graphics-info-preferences.cc: In member function 'short int graphics_info_t::save_preference_file(const string&, short int)':
graphics-info-preferences.cc:75:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<g.preferences_internal.size(); i++) {
                                                ^
graphics-info-preferences.cc: In member function 'void graphics_info_t::make_preferences_internal()':
graphics-info-preferences.cc:436:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<all_items.size(); i++) {
                                  ^
graphics-info-preferences.cc:468:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<all_items.size(); i++) {
                                  ^
graphics-info-preferences.cc: In member function 'void graphics_info_t::preferences_internal_change_value(int, int)':
graphics-info-preferences.cc:631:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<preferences_internal.size(); i++) {
                                             ^
graphics-info-preferences.cc: In member function 'void graphics_info_t::preferences_internal_change_value(int, int, int)':
graphics-info-preferences.cc:642:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<preferences_internal.size(); i++) {
                                             ^
graphics-info-preferences.cc: In member function 'void graphics_info_t::preferences_internal_change_value(int, float)':
graphics-info-preferences.cc:655:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<preferences_internal.size(); i++) {
                                             ^
graphics-info-preferences.cc: In member function 'void graphics_info_t::preferences_internal_change_value(int, float, float, float)':
graphics-info-preferences.cc:667:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<preferences_internal.size(); i++) {
                                             ^
graphics-info-mutate.cc: In member function 'void graphics_info_t::mutate_chain(int, const string&, const string&, bool, bool)':
graphics-info-mutate.cc:358:17: warning: unused variable 'auto_range' [-Wunused-variable]
       short int auto_range = 1;
                 ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-pick.o graphics-info-pick.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-refmac.o graphics-info-refmac.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-render.o graphics-info-render.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-pick.cc:39:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from graphics-info-refmac.cc:63:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-pick.cc:45:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from graphics-info-refmac.cc:76:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
graphics-info-pick.cc: In member function 'coot::Symm_Atom_Pick_Info_t graphics_info_t::symmetry_atom_pick() const':
graphics-info-pick.cc:249:23: warning: variable 'tpos' set but not used [-Wunused-but-set-variable]
       coot::Cartesian tpos = translate_atom(molecules[p_i.imol].atom_sel,
                       ^
graphics-info-pick.cc:76:20: warning: variable 'mid_point' set but not used [-Wunused-but-set-variable]
    coot::Cartesian mid_point = front.mid_point(back);
                    ^
graphics-info-pick.cc: In member function 'void graphics_info_t::rotate_intermediate_atoms_round_screen_x(double)':
graphics-info-pick.cc:743:22: warning: variable 'screen_z' set but not used [-Wunused-but-set-variable]
      coot::Cartesian screen_z = (front - centre);
                      ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::fill_option_menu_with_map_options_internal(GtkWidget*, GtkSignalFunc, std::vector<int>, int)':
graphics-info-refmac.cc:208:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int imap=0; imap<map_molecule_numbers.size(); imap++) {
                                                    ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::fill_option_menu_with_refmac_methods_options(GtkWidget*)':
graphics-info-refmac.cc:293:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<v.size(); i++) {
                          ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::fill_option_menu_with_refmac_phase_input_options(GtkWidget*)':
graphics-info-refmac.cc:325:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<v.size(); i++) {
                          ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::fill_option_menu_with_refmac_file_labels_options(GtkWidget*)':
graphics-info-refmac.cc:470:18: warning: unused variable 'menu' [-Wunused-variable]
       GtkWidget *menu;
                  ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::fill_option_menu_with_refmac_ncycle_options(GtkWidget*)':
graphics-info-refmac.cc:529:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<v.size(); i++) {
                          ^
graphics-info-refmac.cc:541:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<v.size(); i++) {
                          ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::add_refmac_sad_atom(const char*, float, float, float)':
graphics-info-refmac.cc:815:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<graphics_info_t::refmac_sad_atoms.size(); i++) {
                                                          ^
graphics-info-refmac.cc: In member function 'void graphics_info_t::update_refmac_column_labels_frame(GtkWidget*, GtkWidget*, GtkWidget*, GtkWidget*, GtkWidget*, GtkWidget*, GtkWidget*, GtkWidget*)':
graphics-info-refmac.cc:905:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<saved_f_phi_columns->f_cols.size(); i++) {
                                                      ^
graphics-info-refmac.cc:907:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<saved_f_phi_columns->sigf_cols.size(); j++) {
                                                           ^
graphics-info-refmac.cc:924:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<saved_f_phi_columns->r_free_cols.size(); i++) {
                                                           ^
graphics-info-refmac.cc:989:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<saved_f_phi_columns->phi_cols.size(); i++) {
                                                          ^
graphics-info-refmac.cc:998:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<saved_f_phi_columns->weight_cols.size(); i++) {
                                                             ^
graphics-info-refmac.cc:1012:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i<saved_f_phi_columns->hl_cols.size(); i++) {
                                                         ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-render.cc:36:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-render.cc:36:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-residues.o graphics-info-residues.cc
graphics-info-render.cc: In member function 'int coot::raytrace_info_t::renderman_render(std::string)':
graphics-info-render.cc:349:8: warning: variable 'istat' set but not used [-Wunused-but-set-variable]
    int istat = 1;
        ^
graphics-info-render.cc: In member function 'int coot::raytrace_info_t::povray_ray_trace(std::string)':
graphics-info-render.cc:734:29: warning: variable 'camera_translation_cl' set but not used [-Wunused-but-set-variable]
       clipper::Vec3<double> camera_translation_cl = view_centre_cl + tt_cl;
                             ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-residues.cc:26:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-residues.cc:26:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-scripting.o graphics-info-scripting.cc
graphics-info-residues.cc: In member function 'void graphics_info_t::multi_torsion_residues(int, const std::vector<coot::residue_spec_t>&)':
graphics-info-residues.cc:57:12: warning: unused variable 'dict_status' [-Wunused-variable]
       bool dict_status = geom_p->have_dictionary_for_residue_types(residue_types);
            ^
graphics-info-residues.cc: In static member function 'static void graphics_info_t::graphics_ligand_view()':
graphics-info-residues.cc:185:9: warning: unused variable 'ar' [-Wunused-variable]
   float ar = h/w;
         ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-scripting.cc:6:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-scripting.cc:6:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-state.o graphics-info-state.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-info-superpose.o graphics-info-superpose.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-state.cc:35:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-state.cc:35:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-superpose.cc:34:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from graphics-info-superpose.cc:34:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-ligand-view.o graphics-ligand-view.cc
graphics-info-state.cc: In member function 'void graphics_info_t::fill_unsaved_changes_dialog(GtkWidget*) const':
graphics-info-state.cc:967:8: warning: unused variable 'menu_index' [-Wunused-variable]
    int menu_index=0;
        ^
In file included from graphics-ligand-view.hh:22:0,
                 from graphics-ligand-view.cc:26:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
graphics-info-superpose.cc: In static member function 'static void graphics_info_t::fill_superpose_option_menu_with_chain_options(GtkWidget*, int)':
graphics-info-superpose.cc:75:15: warning: variable 'mol_optionmenu' set but not used [-Wunused-but-set-variable]
    GtkWidget *mol_optionmenu = NULL;
               ^
graphics-info-superpose.cc: In member function 'void graphics_info_t::print_horizontal_ssm_sequence_alignment(std::pair<std::basic_string<char>, std::basic_string<char> >) const':
graphics-info-superpose.cc:377:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_lines; i++) {
                             ^
graphics-info-superpose.cc: In member function 'std::pair<std::basic_string<char>, std::basic_string<char> > graphics_info_t::get_horizontal_ssm_sequence_alignment(ssm::Align*, atom_selection_container_t, atom_selection_container_t, CAtom**, CAtom**, int, int) const':
graphics-info-superpose.cc:418:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i1=0; i1<SSMAlign->nsel1; i1++) {
                                            ^
graphics-info-superpose.cc:423:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i2=0; i2<SSMAlign->nsel2; i2++) {
                                            ^
graphics-info-superpose.cc:429:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i1=0; i1<SSMAlign->nsel1; i1++) {
                                         ^
graphics-info-superpose.cc:470:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (s_index == i1) { 
                     ^
graphics-info-superpose.cc:409:8: warning: variable 'previous_t_index' set but not used [-Wunused-but-set-variable]
    int previous_t_index = -1;
        ^
graphics-info-superpose.cc:410:8: warning: unused variable 'previous_s_index' [-Wunused-variable]
    int previous_s_index = -1;
        ^
graphics-ligand-view.cc: In member function 'void graphics_ligand_bond::gl_bond(const lig_build::pos_t&, const lig_build::pos_t&, bool, bool, lig_build::bond_t::bond_type_t)':
graphics-ligand-view.cc:149:11: warning: enumeration value 'DELOC_ONE_AND_A_HALF' not handled in switch [-Wswitch]
    switch (bt) {
           ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o gl-matrix.o gl-matrix.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o gtk-manual.o gtk-manual.cc
gl-matrix.cc: In member function 'std::pair<bool, GL_matrix> GL_matrix::cholesky() const':
gl-matrix.cc:312:11: warning: unused variable 'ic' [-Wunused-variable]
       int ic = gsl_linalg_cholesky_decomp (&m.matrix);
           ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o gtk-widget-conversion-utils.o gtk-widget-conversion-utils.cc
In file included from cc-interface.hh:28:0,
                 from gtk-manual.cc:37:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
gtk-manual.cc: In function 'void on_map_col_sel_cancel_button_clicked(GtkButton*, void**)':
gtk-manual.cc:88:7: warning: unused variable 'imol' [-Wunused-variable]
   int imol = t->imol;
       ^
gtk-manual.cc: In function 'GtkWidget* create_map_colour_selection_window(map_colour_data_type*)':
gtk-manual.cc:104:15: warning: unused variable 'cancel_button' [-Wunused-variable]
    GtkButton *cancel_button;
               ^
gtk-manual.cc:105:15: warning: unused variable 'help_button' [-Wunused-variable]
    GtkButton *help_button;
               ^
gtk-manual.cc: In function 'GtkWidget* create_symmetry_colour_selection_window()':
gtk-manual.cc:159:15: warning: unused variable 'ok_button' [-Wunused-variable]
    GtkButton *ok_button;
               ^
gtk-manual.cc:160:15: warning: unused variable 'cancel_button' [-Wunused-variable]
    GtkButton *cancel_button;
               ^
gtk-manual.cc:161:15: warning: unused variable 'help_button' [-Wunused-variable]
    GtkButton *help_button;
               ^
gtk-manual.cc: In function 'void update_map_scroll_wheel_menu_manual(int, const char*)':
gtk-manual.cc:296:10: warning: unused variable 'text' [-Wunused-variable]
    char *text; 
          ^
gtk-manual.cc: In function 'void update_ramachandran_plot_menu_manual(int, const char*)':
gtk-manual.cc:367:10: warning: unused variable 'text' [-Wunused-variable]
    char *text; 
          ^
gtk-manual.cc: In function 'void update_sequence_view_menu_manual(int, const char*)':
gtk-manual.cc:432:10: warning: unused variable 'text' [-Wunused-variable]
    char *text; 
          ^
gtk-manual.cc: In function 'void display_control_molecule_combo_box(GtkWidget*, const gchar*, int, bool)':
gtk-manual.cc:532:14: warning: variable 'active_item' set but not used [-Wunused-but-set-variable]
   GtkWidget *active_item;
              ^
gtk-manual.cc: In function 'void on_display_control_map_scroll_radio_button_toggled(GtkToggleButton*, gpointer)':
gtk-manual.cc:1296:15: warning: variable 'state' set but not used [-Wunused-but-set-variable]
   const char *state = "inactive";
               ^
gtk-manual.cc: In function 'void on_display_control_map_properties_button_clicked(GtkButton*, gpointer)':
gtk-manual.cc:1375:14: warning: unused variable 'single_map_properties_colour_button' [-Wunused-variable]
   GtkWidget *single_map_properties_colour_button = 
              ^
gtk-manual.cc:1377:14: warning: unused variable 'label' [-Wunused-variable]
   GtkWidget *label = lookup_widget(window, "label114");
              ^
gtk-manual.cc: In function 'void on_display_control_mol_displayed_button_toggled(GtkToggleButton*, gpointer)':
gtk-manual.cc:1474:7: warning: unused variable 'idisplay' [-Wunused-variable]
   int idisplay; 
       ^
gtk-manual.cc: In function 'void on_display_control_mol_active_button_toggled(GtkToggleButton*, gpointer)':
gtk-manual.cc:1523:7: warning: unused variable 'iactive' [-Wunused-variable]
   int iactive; 
       ^
gtk-manual.cc: In function 'GSList* display_cell_chooser_box(GtkWidget*, GSList*, int)':
gtk-manual.cc:1541:14: warning: unused variable 'vbox39' [-Wunused-variable]
   GtkWidget *vbox39;
              ^
gtk-manual.cc:1559:14: warning: unused variable 'hbox34' [-Wunused-variable]
   GtkWidget *hbox34;
              ^
gtk-manual.cc:1560:14: warning: unused variable 'phs_cell_none_radiobutton' [-Wunused-variable]
   GtkWidget *phs_cell_none_radiobutton;
              ^
gtk-manual.cc:1561:14: warning: unused variable 'hbox32' [-Wunused-variable]
   GtkWidget *hbox32;
              ^
gtk-manual.cc:1562:14: warning: unused variable 'phs_cell_choice_ok_button' [-Wunused-variable]
   GtkWidget *phs_cell_choice_ok_button;
              ^
gtk-manual.cc:1563:14: warning: unused variable 'phs_cell_choice_cancel_button' [-Wunused-variable]
   GtkWidget *phs_cell_choice_cancel_button;
              ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c gtk2-interface.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c interface.c
gtk2-interface.c: In function 'create_coot_references_dialog':
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc
gtk2-interface.c:26519:15: warning: variable 'tmp_toolbar_icon_size' set but not used [-Wunused-but-set-variable]
   GtkIconSize tmp_toolbar_icon_size;
               ^
gtk2-interface.c: In function 'create_multi_residue_torsion_dialog':
gtk2-interface.c:27635:7: warning: 'gdk_pixbuf_unref' is deprecated (declared at /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf-core.h:243): Use 'g_object_unref' instead [-Wdeprecated-declarations]
       gdk_pixbuf_unref (multi_residue_torsion_dialog_icon_pixbuf);
       ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o lbg-interface.o lbg-interface.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info.o molecule-class-info.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-maps.o molecule-class-info-maps.cc
In file included from ../lbg/lbg.hh:53:0,
                 from ../lbg/lbg-callbacks.cc:31,
                 from lbg-callbacks-outer.cc:2:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../lbg/lbg.hh:61:0,
                 from ../lbg/lbg-callbacks.cc:31,
                 from lbg-callbacks-outer.cc:2:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from molecule-class-info.cc:46:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info.cc:73:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-maps.cc:41:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from molecule-class-info.h:73,
                 from molecule-class-info-maps.cc:41:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-kdc.o molecule-class-info-kdc.cc
molecule-class-info.cc: In member function 'void molecule_class_info_t::display_ghost_bonds(int)':
molecule-class-info.cc:1743:7: warning: variable 'c' set but not used [-Wunused-but-set-variable]
   int c;
       ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::display_bonds(const graphical_bonds_container&, float)':
molecule-class-info.cc:1810:11: warning: unused variable 'linesdrawn' [-Wunused-variable]
       int linesdrawn = 0;
           ^
molecule-class-info.cc: In member function 'int molecule_class_info_t::add_additional_representation(int, const int&, float, bool, const coot::atom_selection_info_t&, GtkWidget*, const gl_context_info_t&, const coot::protein_geometry*)':
molecule-class-info.cc:2295:99: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if ((display_list_handle_index >= 0) && (display_list_handle_index < display_list_tags.size())) {
                                                                                                   ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::clear_additional_representation(int)':
molecule-class-info.cc:2317:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (add_reps.size() > representation_number) {
                          ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::set_show_additional_representation(int, bool)':
molecule-class-info.cc:2328:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if (add_reps.size() > representation_number) {
                          ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::set_show_all_additional_representations(bool)':
molecule-class-info.cc:2344:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_reps; i++)
                             ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::all_additional_representations_off_except(int, bool)':
molecule-class-info.cc:2353:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_reps; i++)
                             ^
molecule-class-info.cc:2354:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i != rep_no)
                ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::test_label_symm_atom(int)':
molecule-class-info.cc:2469:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i < labelled_symm_atom_index_list.size()) { 
                                                  ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::update_additional_representations(const gl_context_info_t&, const coot::protein_geometry*)':
molecule-class-info.cc:2870:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ((handle >= 0) && (handle < display_list_tags.size())) 
                                                         ^
molecule-class-info.cc: In member function 'int molecule_class_info_t::full_atom_spec_to_atom_index(const string&, int, const string&, const string&, const string&) const':
molecule-class-info.cc:3304:13: warning: variable 'found' set but not used [-Wunused-but-set-variable]
   short int found = 0;
             ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::insert_coords_atoms_into_residue_internal(const atom_selection_container_t&, int)':
molecule-class-info.cc:3948:10: warning: variable 'atom_name' set but not used [-Wunused-but-set-variable]
    char *atom_name;
          ^
molecule-class-info.cc: In member function 'int molecule_class_info_t::add_terminal_residue_using_phi_psi(const string&, int, const string&, float, float)':
molecule-class-info.cc:4101:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat=0; iat<n_residue_atoms; iat++) { 
                                   ^
molecule-class-info.cc: In member function 'bool molecule_class_info_t::close_to_residue(CResidue*, coot::Cartesian) const':
molecule-class-info.cc:4804:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::restore_from_backup(int, const string&)':
molecule-class-info.cc:5858:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (hist_vec_index < history_filename_vec.size() &&
                                                      ^
molecule-class-info.cc: In member function 'void molecule_class_info_t::transform_zone_by(const string&, int, int, const string&, const clipper::RTop_orth&, bool)':
molecule-class-info.cc:7319:10: warning: unused variable 'at' [-Wunused-variable]
   CAtom *at;
          ^
molecule-class-info-maps.cc: In member function 'void molecule_class_info_t::setup_density_surface_material(bool, float, bool)':
molecule-class-info-maps.cc:708:37: warning: narrowing conversion of '((*(*((molecule_class_info_t*)this)->molecule_class_info_t::map_colour)) * 2.9999999999999999e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
       GLfloat  mat_ambient[]   = {.3*map_colour[0][0], 0.3*map_colour[0][1], 0.3*map_colour[0][2], opacity};
                                     ^
molecule-class-info-maps.cc:708:59: warning: narrowing conversion of '((*((*((molecule_class_info_t*)this)->molecule_class_info_t::map_colour) + 8u)) * 2.9999999999999999e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
       GLfloat  mat_ambient[]   = {.3*map_colour[0][0], 0.3*map_colour[0][1], 0.3*map_colour[0][2], opacity};
                                                           ^
molecule-class-info-maps.cc:708:81: warning: narrowing conversion of '((*((*((molecule_class_info_t*)this)->molecule_class_info_t::map_colour) + 16u)) * 2.9999999999999999e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
       GLfloat  mat_ambient[]   = {.3*map_colour[0][0], 0.3*map_colour[0][1], 0.3*map_colour[0][2], opacity};
                                                                                 ^
molecule-class-info-maps.cc:709:50: warning: narrowing conversion of '*(*((molecule_class_info_t*)this)->molecule_class_info_t::map_colour)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
       GLfloat  mat_diffuse[]   = {map_colour[0][0], map_colour[0][1], map_colour[0][2], opacity};
                                                  ^
molecule-class-info-maps.cc:709:68: warning: narrowing conversion of '*((*((molecule_class_info_t*)this)->molecule_class_info_t::map_colour) + 8u)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
       GLfloat  mat_diffuse[]   = {map_colour[0][0], map_colour[0][1], map_colour[0][2], opacity};
                                                                    ^
molecule-class-info-maps.cc:709:86: warning: narrowing conversion of '*((*((molecule_class_info_t*)this)->molecule_class_info_t::map_colour) + 16u)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
       GLfloat  mat_diffuse[]   = {map_colour[0][0], map_colour[0][1], map_colour[0][2], opacity};
                                                                                      ^
molecule-class-info-maps.cc:720:33: warning: narrowing conversion of '((*(*(((molecule_class_info_t*)this)->molecule_class_info_t::map_colour + 4u))) * 2.9999999999999999e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
   GLfloat  mat_ambient[]   = {.3*map_colour[1][0], 0.3*map_colour[1][1], 0.3*map_colour[1][2], opacity};
                                 ^
molecule-class-info-maps.cc:720:55: warning: narrowing conversion of '((*((*(((molecule_class_info_t*)this)->molecule_class_info_t::map_colour + 4u)) + 8u)) * 2.9999999999999999e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
   GLfloat  mat_ambient[]   = {.3*map_colour[1][0], 0.3*map_colour[1][1], 0.3*map_colour[1][2], opacity};
                                                       ^
molecule-class-info-maps.cc:720:77: warning: narrowing conversion of '((*((*(((molecule_class_info_t*)this)->molecule_class_info_t::map_colour + 4u)) + 16u)) * 2.9999999999999999e-1)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
   GLfloat  mat_ambient[]   = {.3*map_colour[1][0], 0.3*map_colour[1][1], 0.3*map_colour[1][2], opacity};
                                                                             ^
molecule-class-info-maps.cc:721:46: warning: narrowing conversion of '*(*(((molecule_class_info_t*)this)->molecule_class_info_t::map_colour + 4u))' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
   GLfloat  mat_diffuse[]   = {map_colour[1][0], map_colour[1][1], map_colour[1][2], opacity};
                                              ^
molecule-class-info-maps.cc:721:64: warning: narrowing conversion of '*((*(((molecule_class_info_t*)this)->molecule_class_info_t::map_colour + 4u)) + 8u)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
   GLfloat  mat_diffuse[]   = {map_colour[1][0], map_colour[1][1], map_colour[1][2], opacity};
                                                                ^
molecule-class-info-maps.cc:721:82: warning: narrowing conversion of '*((*(((molecule_class_info_t*)this)->molecule_class_info_t::map_colour + 4u)) + 16u)' from 'double' to 'GLfloat {aka float}' inside { } is ill-formed in C++11 [-Wnarrowing]
   GLfloat  mat_diffuse[]   = {map_colour[1][0], map_colour[1][1], map_colour[1][2], opacity};
                                                                                  ^
molecule-class-info-maps.cc: In member function 'int molecule_class_info_t::make_map_from_phs(const clipper::Spacegroup&, const clipper::Cell&, std::string)':
molecule-class-info-maps.cc:2768:8: warning: variable 'ncount' set but not used [-Wunused-but-set-variable]
    int ncount = 0; 
        ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-dots.o molecule-class-info-dots.cc
In file included from dots-representation.hh:10:0,
                 from molecule-class-info-dots.cc:2:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
molecule-class-info-dots.cc: In member function 'void coot::dots_representation_info_t::add_dots(int, CMMDBManager*, CMMDBManager*, double, const coot::colour_t&, bool)':
molecule-class-info-dots.cc:102:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat=0; iat<n_atoms; iat++) {
                                 ^
molecule-class-info-dots.cc:120:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_atoms_exclude; iat++) {
                                    ^
molecule-class-info-dots.cc:144:12: warning: unused variable 'atom_radius_squard' [-Wunused-variable]
     double atom_radius_squard = atom_radius * atom_radius;
            ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-kdc.cc:36:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from molecule-class-info.h:73,
                 from molecule-class-info-kdc.cc:36:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-other.o molecule-class-info-other.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from molecule-class-info-other.cc:65:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info-other.cc:68:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-build.o molecule-class-info-build.cc
molecule-class-info-other.cc: In member function 'std::vector<std::pair<CAtom*, float> > coot::dots_representation_info_t::solvent_exposure(int, CMMDBManager*) const':
molecule-class-info-other.cc:120:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_atoms; iat++) {
                                    ^
molecule-class-info-other.cc:154:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int i_all=0; i_all<n_atoms_all; i_all++) {
                                         ^
molecule-class-info-other.cc: In member function 'graphical_bonds_container molecule_class_info_t::make_environment_bonds_box(int, coot::protein_geometry*) const':
molecule-class-info-other.cc:732:18: warning: unused variable 'SelResidues' [-Wunused-variable]
       PPCResidue SelResidues;
                  ^
molecule-class-info-other.cc:733:11: warning: unused variable 'nSelResdues' [-Wunused-variable]
       int nSelResdues;
           ^
molecule-class-info-other.cc:735:11: warning: unused variable 'ires' [-Wunused-variable]
       int ires = point_atom_p->GetSeqNum();
           ^
molecule-class-info-other.cc:736:19: warning: unused variable 'chain_id' [-Wunused-variable]
       const char *chain_id = point_atom_p->GetChainID();
                   ^
molecule-class-info-other.cc: In member function 'short int molecule_class_info_t::delete_residue(int, const string&, int, const string&)':
molecule-class-info-other.cc:986:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int imod=1; imod<=n_models; imod++) {
                                    ^
molecule-class-info-other.cc:993:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if ((imod == model_number) || (model_number == MinInt4)) { 
                    ^
molecule-class-info-other.cc: In member function 'short int molecule_class_info_t::delete_residue_hydrogens(const string&, int, const string&, const string&)':
molecule-class-info-other.cc:1090:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int iat=0; iat<nResidueAtoms; iat++) {
                                     ^
molecule-class-info-other.cc: In member function 'int molecule_class_info_t::delete_hydrogens()':
molecule-class-info-other.cc:1647:8: warning: unused variable 'n_deleted' [-Wunused-variable]
    int n_deleted = 0;
        ^
molecule-class-info-other.cc: In member function 'float molecule_class_info_t::auto_fit_best_rotamer(int, int, const string&, const string&, const string&, int, int, float, const coot::protein_geometry&)':
molecule-class-info-other.cc:1726:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (imol_map < graphics_info_t::molecules.size()) {
                                                  ^
molecule-class-info-other.cc: In member function 'std::pair<bool, float> molecule_class_info_t::backrub_rotamer(const string&, int, const string&, const string&, const coot::protein_geometry&)':
molecule-class-info-other.cc:2069:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (imol_map < graphics_info_t::molecules.size()) {
                                                      ^
molecule-class-info-other.cc: In member function 'CResidue* molecule_class_info_t::get_first_residue()':
molecule-class-info-other.cc:2285:10: warning: unused variable 'at' [-Wunused-variable]
   CAtom *at;
          ^
molecule-class-info-other.cc: In constructor 'coot::go_to_residue_string_info_t::go_to_residue_string_info_t(const string&, CMMDBManager*)':
molecule-class-info-other.cc:2419:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<l; i++) { 
                    ^
molecule-class-info-other.cc: In member function 'coot::ray_trace_molecule_info molecule_class_info_t::fill_raster_model_info()':
molecule-class-info-other.cc:3902:24: warning: statement has no effect [-Wunused-value]
         bonds_box_type == coot::NORMAL_BONDS;
                        ^
molecule-class-info-other.cc: In member function 'std::pair<bool, std::basic_string<char> > molecule_class_info_t::split_residue(int, int)':
molecule-class-info-other.cc:4189:11: warning: variable 'do_intermediate_atoms' set but not used [-Wunused-but-set-variable]
       int do_intermediate_atoms = 0;
           ^
molecule-class-info-other.cc: In member function 'int molecule_class_info_t::renumber_residue_range(const string&, int, int, int)':
molecule-class-info-other.cc:5207:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int ichres=0; ichres<chain_n_residues; ichres++) {
                                      ^
molecule-class-info-other.cc: In member function 'std::vector<coot::atom_spec_t> molecule_class_info_t::find_water_baddies_OR(float, const clipper::Xmap<float>&, float, float, float, float, short int, short int)':
molecule-class-info-other.cc:5737:19: warning: unused variable 'd' [-Wunused-variable]
            double d;
                   ^
molecule-class-info-other.cc:5739:19: warning: unused variable 'dc_sqrd' [-Wunused-variable]
            double dc_sqrd = dist_to_atoms_min * dist_to_atoms_min;
                   ^
molecule-class-info-other.cc: In member function 'int molecule_class_info_t::read_shelx_ins_file(const string&)':
molecule-class-info-other.cc:5848:11: warning: unused variable 'udd_afix_handle' [-Wunused-variable]
       int udd_afix_handle = p.mol->GetUDDHandle(UDR_ATOM, "shelx afix");
           ^
molecule-class-info-other.cc: In member function 'coot::display_list_object_info molecule_class_info_t::make_ball_and_stick(const string&, float, float, bool, bool, coot::display_list_object_info, const coot::protein_geometry*)':
molecule-class-info-other.cc:6119:11: warning: unused variable 'bgcolor' [-Wunused-variable]
   GLfloat bgcolor[4]={bond_colour_internal[0],
           ^
molecule-class-info-other.cc:6099:16: warning: unused variable 'mat_specular' [-Wunused-variable]
       GLfloat  mat_specular[]  = {0.8, 0.8, 0.8, 1.0};
                ^
molecule-class-info-other.cc:6100:16: warning: unused variable 'mat_ambient' [-Wunused-variable]
       GLfloat  mat_ambient[]   = {0.2, 0.2, 0.2, 1.0};
                ^
molecule-class-info-other.cc:6101:16: warning: unused variable 'mat_diffuse' [-Wunused-variable]
       GLfloat  mat_diffuse[]   = {0.7, 0.7, 0.7, 1.0};
                ^
molecule-class-info-other.cc:6102:16: warning: unused variable 'mat_shininess' [-Wunused-variable]
       GLfloat  mat_shininess[] = {50.0};
                ^
molecule-class-info-other.cc:6058:8: warning: unused variable 'i' [-Wunused-variable]
    int i = -1;
        ^
molecule-class-info-other.cc: In member function 'void molecule_class_info_t::change_chain_id_with_residue_range_helper_insert_or_add(CChain*, CResidue*)':
molecule-class-info-other.cc:6754:8: warning: unused variable 'target_res_seq_num' [-Wunused-variable]
    int target_res_seq_num = resno_new_residue; // simply ignore ins codes :)
        ^
molecule-class-info-other.cc: In member function 'int molecule_class_info_t::cis_trans_convert(CResidue**, CResidue**, CResidue**)':
molecule-class-info-other.cc:6997:17: warning: variable 'is_cis_flag' set but not used [-Wunused-but-set-variable]
       short int is_cis_flag = 0;
                 ^
molecule-class-info-other.cc: In member function 'void molecule_class_info_t::draw_dots()':
molecule-class-info-other.cc:7713:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int iset=0; iset<dots.size(); iset++) {
                                       ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-build.cc:31:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from molecule-class-info.h:73,
                 from molecule-class-info-build.cc:31:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
molecule-class-info-build.cc: In member function 'ProteinDB::Chain molecule_class_info_t::make_fragment_chain(const std::vector<coot::residue_spec_t>&) const':
molecule-class-info-build.cc:72:11: warning: unused variable 'i_loop_res' [-Wunused-variable]
       int i_loop_res=0;
           ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-mutate.o molecule-class-info-mutate.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info-mutate.cc:50:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info-mutate.cc:50:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-residues.o molecule-class-info-residues.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info-residues.cc:41:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info-residues.cc:41:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
molecule-class-info-residues.cc: In member function 'std::pair<bool, std::basic_string<char> > molecule_class_info_t::sprout_hydrogens(const string&, int, const string&, const coot::protein_geometry&)':
molecule-class-info-residues.cc:187:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0; i<n_residue_atoms; i++)
                             ^
molecule-class-info-residues.cc:251:9: warning: variable 'n_restraints' set but not used [-Wunused-but-set-variable]
     int n_restraints = restraints.make_restraints(geom, flags, do_torsions,
         ^
molecule-class-info-residues.cc: In member function 'void molecule_class_info_t::sprout_hydrogens_transfer_hydrogen_positions(CResidue*, CResidue*, const string&)':
molecule-class-info-residues.cc:360:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int iat_1=0; iat_1<n_residue_atoms_1; iat_1++) {
                                     ^
molecule-class-info-residues.cc:367:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int iat_2=0; iat_2<n_residue_atoms_2; iat_2++) {
                                       ^
molecule-class-info-residues.cc: In member function 'clipper::Coord_orth molecule_class_info_t::get_vector(const coot::residue_spec_t&, const coot::residue_spec_t&) const':
molecule-class-info-residues.cc:471:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<c_n_residue_atoms; iat++) {
                                ^
molecule-class-info-residues.cc:479:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int jat=0; jat<n_n_residue_atoms; jat++) {
                                ^
molecule-class-info-residues.cc:461:10: warning: unused variable 'min_dist' [-Wunused-variable]
   double min_dist = 42e32;
          ^
molecule-class-info-residues.cc: In member function 'coot::rama_score_t molecule_class_info_t::get_all_molecule_rama_score() const':
molecule-class-info-residues.cc:566:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (imod<=atom_sel.mol->GetNumberOfModels()) {
                                                 ^
molecule-class-info-residues.cc:575:20: warning: unused variable 'sse' [-Wunused-variable]
                int sse = residue_p->SSE;
                    ^
molecule-class-info-residues.cc: In member function 'void coot::animated_ligand_interactions_t::draw(CMMDBManager*, const gl_context_info_t&, const long int&) const':
molecule-class-info-residues.cc:832:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int ipart=0; ipart<n_parts; ipart++) {
                                    ^
molecule-class-info-residues.cc:791:12: warning: unused variable 'ambientLight' [-Wunused-variable]
   GLfloat  ambientLight[] = { 0.2f, 0.2f, 0.2f, 0.5f };
            ^
molecule-class-info-residues.cc:792:12: warning: unused variable 'diffuseLight' [-Wunused-variable]
   GLfloat  diffuseLight[] = { 0.2f, 0.2f, 0.2f, 0.5f };
            ^
molecule-class-info-residues.cc:793:11: warning: unused variable 'specularLight' [-Wunused-variable]
   GLfloat specularLight[] = { 0.2f, 0.2f, 0.2f, 0.5f };
           ^
molecule-class-info-residues.cc: In member function 'std::pair<bool, clipper::Coord_orth> molecule_class_info_t::residue_centre(CResidue*) const':
molecule-class-info-residues.cc:933:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                    ^
molecule-class-info-residues.cc: In member function 'coot::new_centre_info_t molecule_class_info_t::new_ligand_centre(const clipper::Coord_orth&, int) const':
molecule-class-info-residues.cc:1029:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (current_centre_index == (ligand_centres.size()-1)) {
                                                          ^
molecule-class-info-residues.cc: In constructor 'coot::dict_link_info_t::dict_link_info_t(CResidue*, CResidue*, const string&, const coot::protein_geometry&)':
molecule-class-info-residues.cc:1213:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (unsigned int iat1=0; iat1<n_residue_atoms_1; iat1++) { 
                                        ^
molecule-class-info-residues.cc:1220:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        for (unsigned int iat2=0; iat2<n_residue_atoms_2; iat2++) { 
                                       ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-refine.o molecule-class-info-refine.cc
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-refine.cc:11:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from molecule-class-info.h:73,
                 from molecule-class-info-refine.cc:11:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-kk.o molecule-class-info-kk.cc
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-kk.cc:25:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from molecule-class-info.h:73,
                 from molecule-class-info-kk.cc:25:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-surface.o molecule-class-info-surface.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from molecule-class-info-surface.cc:35:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-ncs.o molecule-class-info-ncs.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o molecule-class-info-widget-work.o molecule-class-info-widget-work.cc
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from molecule-class-info-surface.cc:38:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from molecule-class-info-ncs.cc:42:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o nsv.o nsv.cc
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-ncs.cc:44:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from coot-align.hh:2:0,
                 from molecule-class-info.h:56,
                 from molecule-class-info-widget-work.cc:32:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from molecule-class-info.h:73,
                 from molecule-class-info-widget-work.cc:32:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
molecule-class-info-ncs.cc: In member function 'int molecule_class_info_t::test_function()':
molecule-class-info-ncs.cc:692:20: warning: unused variable 'g' [-Wunused-variable]
    graphics_info_t g;
                    ^
molecule-class-info-ncs.cc: In member function 'void molecule_class_info_t::copy_chain(const string&, const string&)':
molecule-class-info-ncs.cc:1489:13: warning: variable 'done_copy_flag' set but not used [-Wunused-but-set-variable]
   short int done_copy_flag = 0;
             ^
In file included from nsv.hh:47:0,
                 from nsv.cc:38:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o pick.o pick.cc
nsv.cc: In member function 'void exptl::nsv::mol_to_canvas(CMMDBManager*, int, double)':
nsv.cc:281:8: warning: unused variable 'ss_status' [-Wunused-variable]
    int ss_status = model_p->CalcSecStructure(1);
        ^
nsv.cc: In member function 'std::vector<exptl::nsv::chain_length_residue_units_t> exptl::nsv::get_residue_counts(CMMDBManager*) const':
nsv.cc:476:14: warning: unused variable 'at' [-Wunused-variable]
       CAtom *at;
              ^
nsv.cc: In member function 'void exptl::nsv::origin_marker()':
nsv.cc:613:22: warning: variable 'item' set but not used [-Wunused-but-set-variable]
       GtkCanvasItem *item;
                      ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o protein_db-interface.o protein_db-interface.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from pick.cc:39:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from pick.cc:45:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from protein_db-interface.cc:3:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
protein_db-interface.cc: In function 'std::vector<CResidue*> add_chain_to_molecule(const ProteinDB::Chain&, const string&, int, CMMDBManager*)':
protein_db-interface.cc:43:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int ires=0; ires<chain.size(); ires++) { 
                                              ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c read-phs.c
read-phs.c: In function 'try_read_phs_file':
read-phs.c:47:8: warning: unused variable 'is_pha_extension' [-Wunused-variable]
    int is_pha_extension;  /* pha is a phs file too (shelx) */
        ^
read-phs.c: In function 'phs_pdb_cell_symm':
read-phs.c:213:8: warning: variable 'imol' set but not used [-Wunused-but-set-variable]
    int imol; 
        ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c read-cif.c
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rama_mousey.o rama_mousey.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rama_plot.o rama_plot.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o restraints-editor.o restraints-editor.cc
In file included from rama_plot.hh:27:0,
                 from rama_plot.cc:44:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from rama_plot.hh:27:0,
                 from rama_mousey.cc:32:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
rama_plot.cc: In member function 'void coot::rama_plot::big_square(int, const string&, int, const string&)':
rama_plot.cc:251:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (model_number < phi_psi_model_sets.size()) {
                                                  ^
rama_plot.cc: In member function 'void coot::rama_plot::display_background()':
rama_plot.cc:420:14: warning: variable 'doit' set but not used [-Wunused-but-set-variable]
    short int doit;
              ^
rama_plot.cc: In member function 'coot::rama_stats_container_t coot::rama_plot::draw_phi_psi_points()':
rama_plot.cc:842:14: warning: unused variable 'as_white_flag' [-Wunused-variable]
    short int as_white_flag = 0;
              ^
rama_plot.cc: In member function 'gint coot::rama_plot::button_press_conventional(GtkWidget*, GdkEventButton*)':
rama_plot.cc:1132:20: warning: variable 'state' set but not used [-Wunused-but-set-variable]
    GdkModifierType state;
                    ^
rama_plot.cc: In member function 'gint coot::rama_plot::button_press_editphipsi(GtkWidget*, GdkEventButton*)':
rama_plot.cc:1180:20: warning: variable 'state' set but not used [-Wunused-but-set-variable]
    GdkModifierType state;
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o sdf-interface.o sdf-interface.cc
rama_plot.cc: In member function 'void coot::rama_plot::draw_2_phi_psi_sets_on_canvas(CMMDBManager*, CMMDBManager*, std::string, std::string)':
rama_plot.cc:1740:8: warning: unused variable 'imod' [-Wunused-variable]
    int imod = 1;
        ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c support.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c support-gtk2-extras.c
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from restraints-editor.cc:51:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from restraints-editor.cc:51:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o testing.o testing.cc
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c trackball.c
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o sequence-view.o sequence-view.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from testing.hh:27,
                 from testing.cc:25:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../coot-utils/coot-coord-extras.hh:30:0,
                 from testing.hh:30,
                 from testing.cc:25:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
testing.cc: In function 'int test_wiggly_ligands()':
testing.cc:472:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (ms.size() != wiggly_ligand_n_samples) {
                        ^
testing.cc: In function 'residue_selection_t testing_func_probabilities_refine_fragment(atom_selection_container_t, CResidue**, int, const string&, int, coot::protein_geometry, bool, int, bool, bool)':
testing.cc:544:14: warning: unused variable 'do_link_torsions' [-Wunused-variable]
    short int do_link_torsions = 0;
              ^
testing.cc:562:8: warning: unused variable 'nrestraints' [-Wunused-variable]
    int nrestraints = 
        ^
testing.cc: In function 'int test_ramachandran_probabilities()':
testing.cc:623:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<resnos.size(); i++) { 
                                ^
testing.cc:622:8: warning: unused variable 'n_correct' [-Wunused-variable]
    int n_correct = 0; 
        ^
testing.cc: In function 'int kdc_torsion_test()':
testing.cc:752:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int i = 0; i < dparams.size(); i++ ) {
                                    ^
testing.cc:769:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int i = 0; i < dparams.size(); i++ ) {
                                    ^
testing.cc: In function 'int test_add_atom()':
testing.cc:1012:11: warning: unused variable 'nres' [-Wunused-variable]
       int nres = chain_p->GetNumberOfResidues();
           ^
testing.cc:1014:14: warning: unused variable 'at' [-Wunused-variable]
       CAtom *at;
              ^
testing.cc: In function 'int test_segid_exchange()':
testing.cc:1173:9: warning: unused variable 'ifound' [-Wunused-variable]
    bool ifound = 0;
         ^
testing.cc: In function 'int test_ligand_conformer_torsion_angles()':
testing.cc:1355:8: warning: unused variable 'status' [-Wunused-variable]
    int status = 0;
        ^
testing.cc: In function 'int test_coot_atom_tree()':
testing.cc:1524:8: warning: variable 'geom_stat' set but not used [-Wunused-but-set-variable]
    int geom_stat = geom.init_refmac_mon_lib(greg_test(cif_file_name), 0);
        ^
testing.cc:1536:9: warning: unused variable 'ifound' [-Wunused-variable]
    bool ifound = 0;
         ^
testing.cc:1538:8: warning: unused variable 'imod' [-Wunused-variable]
    int imod = 1;
        ^
testing.cc: In function 'int test_coot_atom_tree_2()':
testing.cc:1652:9: warning: unused variable 'tat_result' [-Wunused-variable]
    bool tat_result = tat.test_atom_vec(contact_indices);
         ^
testing.cc: In function 'CResidue* test_get_residue(CMMDBManager*, const string&, int)':
testing.cc:1722:14: warning: unused variable 'res' [-Wunused-variable]
    CResidue *res = 0;
              ^
testing.cc: In function 'bool test_rotate_atom_angle(const string&, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&, const clipper::Coord_orth&, double)':
testing.cc:2031:11: warning: unused variable 'bdlen2' [-Wunused-variable]
    double bdlen2 = clipper::Coord_orth::length(D_pt, rotate_pt_2);
           ^
testing.cc:2032:11: warning: unused variable 'cdlen' [-Wunused-variable]
    double cdlen = clipper::Coord_orth::length(D_pt, C_pt);
           ^
testing.cc: In function 'int test_geometry_distortion_info_type()':
testing.cc:2241:13: warning: unused variable 'x' [-Wunused-variable]
         int x = 2; 
             ^
testing.cc:2250:9: warning: unused variable 'x' [-Wunused-variable]
     int x = 2;
         ^
testing.cc: In function 'int test_copy_cell_symm_orig_scale_headers()':
testing.cc:2385:8: warning: unused variable 'r' [-Wunused-variable]
    int r = 0;
        ^
testing.cc: In function 'int test_residue_atom_renaming()':
testing.cc:2484:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++)
                                ^
testing.cc:2491:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++)
                                ^
testing.cc:2501:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++)
                                ^
testing.cc:2508:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (unsigned int i=0; i<n_residue_atoms; i++) {
                                ^
testing.cc: In function 'int test_position_residue_by_internal_coords()':
testing.cc:2647:8: warning: unused variable 'idealised_flag' [-Wunused-variable]
    int idealised_flag = 1;
        ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from ../ligand/monomer-utils.hh:33,
                 from ../ligand/chi-angles.hh:25,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from sequence-view.cc:36:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
testing.cc: In function 'int test_multi_residue_torsion()':
testing.cc:2750:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int i=0; i<n_selected_atoms; i++) { 
                            ^
testing.cc: In function 'int test_torsions_from_residue_selection()':
testing.cc:2774:20: warning: unused variable 'g' [-Wunused-variable]
    graphics_info_t g;
                    ^
In file included from ../ligand/chi-angles.hh:27:0,
                 from ../ligand/rotamer.hh:28,
                 from graphics-info.h:68,
                 from sequence-view.cc:36:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c seq-view-interface.c
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o user-mods.o user-mods.cc
sequence-view.cc: In member function 'void coot::sequence_view::draw_debugging_box() const':
sequence-view.cc:135:19: warning: variable 'item' set but not used [-Wunused-but-set-variable]
    GtkCanvasItem *item;
                   ^
In file included from user-mods.cc:11:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
user-mods.cc: In member function 'void coot::flips_container::store(const std::vector<std::basic_string<char> >&)':
user-mods.cc:129:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int iline=0; iline<lines.size(); iline++) {
                                      ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o xmap-utils.o xmap-utils.cc
swig -o coot_wrap_python_pre_gtk2.cc -DCOOT_USE_GTK2_INTERFACE -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DUSE_LIBCURL -I../src -shadow -python -c++ ../src/coot.i && mv coot.py coot_gtk2.py
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o density-score-by-residue-src.o density-score-by-residue-src.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o fix-nomenclature.o fix-nomenclature.cc
In file included from density-score-by-residue-src.cc:45:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o align.o align.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from density-score-by-residue-src.cc:51:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from align.cc:26:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from align.cc:31:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
align.cc: In function 'coot::chain_mutation_info_container_t align_on_chain(CChain*, CResidue**, int, const string&)':
align.cc:129:13: warning: unused variable 'wgap' [-Wunused-variable]
    realtype wgap = 0.0;
             ^
align.cc:130:13: warning: unused variable 'wspace' [-Wunused-variable]
    realtype wspace = -1.0;
             ^
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from fix-nomenclature.cc:6:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-chol.o test-chol.cc
/bin/sh ../src/post-process-coot-wrap-guile.sh "/usr/bin/guile1.8-config" gtk1 coot_wrap_guile_pre_gtk1.cc coot_wrap_guile_gtk1.cc
guile_config: /usr/bin/guile1.8-config
guile_version: guile1.8-config - Guile version 1.8.8
gtk2: gtk1
sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/SCM_STRINGP/scm_is_string/ -e s/SCM_STRING_LENGTH/scm_c_string_length/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ -e /.libguile.h./{x;s/.*/#include <cstdio>/;G;} coot_wrap_guile_pre_gtk1.cc ..to.. coot_wrap_guile_pre_gtk1.cc.tmp
/bin/sh ../src/post-process-coot-wrap-guile.sh "/usr/bin/guile1.8-config" gtk2 coot_wrap_guile_pre_gtk2.cc coot_wrap_guile_gtk2.cc
adding gtk2 and guile ifdefs from coot_wrap_guile_pre_gtk1.cc.tmp coot_wrap_guile_gtk1.cc
/bin/sh ../src/post-process-coot-wrap-python.sh  gtk2 coot_wrap_python_pre_gtk2.cc coot_wrap_python_gtk2.cc
guile_config: /usr/bin/guile1.8-config
guile_version: guile1.8-config - Guile version 1.8.8
gtk2: gtk2
sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/SCM_STRINGP/scm_is_string/ -e s/SCM_STRING_LENGTH/scm_c_string_length/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ -e /.libguile.h./{x;s/.*/#include <cstdio>/;G;} coot_wrap_guile_pre_gtk2.cc ..to.. coot_wrap_guile_pre_gtk2.cc.tmp
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-coot-align align.o coot-align.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   
adding gtk2 and guile ifdefs from coot_wrap_guile_pre_gtk2.cc.tmp coot_wrap_guile_gtk2.cc
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-cholesky test-chol.o gl-matrix.o ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../geometry/libcoot-geometry.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
cp coot_gtk2.py coot.py
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk1.cc
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-19-python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-coot-align align.o coot-align.o  ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -fopenmp -pthread
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot_wrap_guile_gtk2.o coot_wrap_guile_gtk2.cc
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../protein_db -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootilus -I../cootaneer -I../lidia-core -I../libgtkgraph -I../goograph -I../lbg   -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/atk-1.0 -I/usr/include/harfbuzz    -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz  -DHAVE_SSMLIB   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include  -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz                      -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o coot_wrap_python_gtk2.o coot_wrap_python_gtk2.cc
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o density-score-by-residue-real density-score-by-residue-src.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-19-python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-cholesky test-chol.o gl-matrix.o  ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../geometry/.libs/libcoot-geometry.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lm -fopenmp -pthread
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/libcoot-ligand.la ../db-main/libcoot-db-main.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la  -lgsl -lgslcblas -lm -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb  		 
coot_wrap_guile_gtk2.cc: In function 'void SWIG_Guile_SetModule(swig_module_info*)':
coot_wrap_guile_gtk2.cc:1198:7: warning: unused variable 'variable' [-Wunused-variable]
   SCM variable;
       ^
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-19-python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/density-score-by-residue-real density-score-by-residue-src.o  ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lm -fopenmp -pthread
In file included from coot_wrap_guile_gtk2.cc:1412:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-19-python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o  ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.7/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs/libccp4mg-utils.so ../db-main/.libs/libcoot-db-main.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so -lgsl -lgslcblas -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -fopenmp -pthread
coot_wrap_guile_gtk2.cc: In function 'scm_unused_struct* _wrap_new_vector_string(SCM)':
coot_wrap_guile_gtk2.cc:1634:24: warning: unused variable 'x' [-Wunused-variable]
           std::string* x;
                        ^
coot_wrap_guile_gtk2.cc:1643:22: warning: unused variable 'x' [-Wunused-variable]
         std::string* x;
                      ^
In file included from coot_wrap_python_gtk2.cc:3511:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-19-python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE  -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o coot-real main.o svn-revision.o c-inner-main.o c-interface-analysis.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o c-interface-mmdb.o c-interface-mogul.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o c-interface-preferences.o c-interface-refine.o c-interface-residues.o c-interface-scm.o c-interface-sfs.o c-interface-superpose.o c-interface-validate.o c-interface-view.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o c-interface.o c-interface-test.o callbacks.o cmtz-interface.o command-line.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o drag-and-drop.o geometry-graphs.o get-residue.o flev.o generic-objects.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o graphics-info-residues.o graphics-info-scripting.o graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-other.o molecule-class-info-build.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o protein_db-interface.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o sdf-interface.o support.o support-gtk2-extras.o testing.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o coot_wrap_python_gtk2.o -fopenmp ../lbg/libcoot-lidia.la ../ligand/libcoot-ligand.la ../lidia-core/libcoot-lidia-core.la ../goograph/libcoot-goograph.la ../libgtkgraph/libcoot-gtkgraph.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../db-main/libcoot-db-main.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libccp4mg-surface.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../analysis/libcoot-analysis.la ../protein_db/libcoot-protein-db.la ../cootilus/libcootilus.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la  		  -pthread  -lguile  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lssm -lmmdb   -lmmdb   -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -lutil  -Wl,--export-dynamic -pthread -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgmodule-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lglut  -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0    -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lgsl -lgslcblas -lm  -lcurl     -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0   
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-19-python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/coot-real main.o svn-revision.o c-inner-main.o c-interface-analysis.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o c-interface-mmdb.o c-interface-mogul.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o c-interface-preferences.o c-interface-refine.o c-interface-residues.o c-interface-scm.o c-interface-sfs.o c-interface-superpose.o c-interface-validate.o c-interface-view.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o c-interface.o c-interface-test.o callbacks.o cmtz-interface.o command-line.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o drag-and-drop.o geometry-graphs.o get-residue.o flev.o generic-objects.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o graphics-info-residues.o graphics-info-scripting.o graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-other.o molecule-class-info-build.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o protein_db-interface.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o sdf-interface.o support.o support-gtk2-extras.o testing.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o coot_wrap_python_gtk2.o -fopenmp -pthread -Wl,-export-dynamic -Wl,--export-dynamic -pthread  ../lbg/.libs/libcoot-lidia.so ../ligand/.libs/libcoot-ligand.so ../lidia-core/.libs/libcoot-lidia-core.so ../goograph/.libs/libcoot-goograph.so ../libgtkgraph/.libs/libcoot-gtkgraph.so ../density-contour/.libs/libcoot-isosurface.so ../build/.libs/libcoot-cabuild.so ../skeleton/.libs/libcoot-skeleton.so /builddir/build/BUILD/coot-0.7/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so ../db-main/.libs/libcoot-db-main.so ../high-res/.libs/libcoot-high-res.so /builddir/build/BUILD/coot-0.7/ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.7/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs/libccp4mg-utils.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../coot-surface/.libs/libcoot-surface.so /builddir/build/BUILD/coot-0.7/surface/.libs/libccp4mg-surface.so ../surface/.libs/libccp4mg-surface.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../protein_db/.libs/libcoot-protein-db.so ../cootilus/.libs/libcootilus.so ../cootaneer/.libs/libcootaneer.so ../compat/.libs/libcoot-compat.so -lguile -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lssm -lmmdb -lpthread -ldl -lpython2.7 -lutil -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXt -lSM -lICE -lpangox-1.0 -lX11 -lgmodule-2.0 -lglut -lXmu -lgnomecanvas-2 -lart_lgpl_2 -lgsl -lgslcblas -lm -lcurl -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -fopenmp -pthread
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~/build/BUILD/coot-0.7/doc ~/build/BUILD/coot-0.7
+ pushd doc
+ texi2pdf coot-user-manual.texi
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[2] [-1] Chapter 1
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 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text
it Acta Crys-tal-lo-graph-ica Sec-tion 
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[4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12]
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[]@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine-
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[]@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr
eferences -> Smooth
[15] [16] Chapter 4 [17] [18] [19] [20]
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[]@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i
d m11 m12 m13
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Chapter 5 [26] [27] [28]
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[][][] |
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alt-loc
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[]@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f
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[37]
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[]@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling 
-> Replace
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[]@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr
m '[] and a dic-tio-nary file
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o-start
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@textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m
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Chapter 7 [54] [55] [56] [57] Chapter 8 [58]
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[]@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch
arge @textrm field in the
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[143]
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 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues
 in the
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[204] [205] [206] [207] [208] [209]pdfTeX warning (ext4): destination with the 
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l.12236 @section Surfaces
                          [210] [211] [212] [213] [214] [215] [216] [217])
Chapter 12 [218] Chapter 13 [219] (Concept Index) [220] (Function Index)
[221] [222] )
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Output written on coot-user-manual.pdf (225 pages, 680086 bytes).
Transcript written on coot-user-manual.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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[-29] [-30]) [-31] (./coot-user-manual.toc) (./coot-user-manual.toc) Chapter 1
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 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text
it Acta Crys-tal-lo-graph-ica Sec-tion 
[1] [2] [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12]
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[]@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine-
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[15] [16] Chapter 4 [17] [18] [19] [20]
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[]@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i
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Chapter 5 [26] [27] [28]
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[29] [30]
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[]@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol
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[34] [35] [36]
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[]@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f
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[37]
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[]@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling 
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[]@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr
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[38] [39] [40] [41] [42]
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[]@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c
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[43] [44] [45] [46] Chapter 6 [47]
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@textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m
ap
Chapter 7 [54] [55] [56] [57] Chapter 8 [58]
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[]@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch
arge @textrm field in the
Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (./c-interface_8h.texi
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l.12236 @section Surfaces
                          [210] [211] [212] [213] [214] [215] [216] [217])
Chapter 12 [218] Chapter 13 [219] (Concept Index) [220] (./coot-user-manual.cps
[221] [222]) (Function Index) [223] (./coot-user-manual.fns [224] [225]
[226] [227] [228] [229] [230] [231] [232] [233] [234]) [235] )
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This is `epsf.tex' v2.7.4 <14 February 2011>
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[-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28]
[-29] [-30]) [-31] (./coot-user-manual.toc) (./coot-user-manual.toc) Chapter 1
Underfull \hbox (badness 2556) in paragraph at lines 366--369
 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text
it Acta Crys-tal-lo-graph-ica Sec-tion 
[1] [2] [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12]
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[]@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine-
[13] [14]
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[]@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr
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[15] [16] Chapter 4 [17] [18] [19] [20]
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[]@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i
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Chapter 5 [26] [27] [28]
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[][][] |
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@textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this 
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[]@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol
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[34] [35] [36]
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[]@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f
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[37]
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[]@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling 
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[]@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr
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[38] [39] [40] [41] [42]
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[43] [44] [45] [46] Chapter 6 [47]
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[]@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin
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[51]
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@textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m
ap
Chapter 7 [54] [55] [56] [57] Chapter 8 [58]
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[]@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch
arge @textrm field in the
Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (./c-interface_8h.texi
[64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78]
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                          [210] [211] [212] [213] [214] [215] [216] [217])
Chapter 12 [218] Chapter 13 [219] (Concept Index) [220] (./coot-user-manual.cps
[221] [222]) (Function Index) [223] (./coot-user-manual.fns [224] [225]
[226] [227] [228] [229] [230] [231] [232] [233] [234]) [235] )
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</usr/share/texlive/texmf-dist/dvips/base/texps.pro>. 
</usr/share/texlive/texmf-dist/fonts/type1/urw/palatino/uplri8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/palatino/uplr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/euler/eurm10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/palatino/uplb8a.pfb>[1] [2] 
ps2pdf crib-sheet.ps
cp crib-sheet.pdf coot-keys-and-buttons.pdf
~/build/BUILD/coot-0.7
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.R8Z42b
+ popd
+ exit 0
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386
++ dirname /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386
+ cd coot-0.7
+ rm -rf /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386
+ make install DESTDIR=/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386 'INSTALL=install -p'
Making install in auxil
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
Making install in catcheck
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
Making install in rama
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
Making install in sec-str
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
Making install in strand-analysis
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
Making install in vectors
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
Making install in scheme
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/scheme'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/scheme'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/scheme'
 install -p -m 644 0-auto-rot.scm coot-utils.scm get-ebi.scm mutate.scm background-demo.scm demo-script.scm gtkin.scm my-readline.scm bit.scm extra-top-level.scm hello.scm raster3d.scm brute-lsqman.scm file-utils.scm junk.scm refmac.scm coot-gui.scm filter.scm libcheck.scm simple.scm coot.scm get-ebi.save.scm local-code.scm trivial.scm gap.scm remote-control.scm povray.scm coot-lsq.scm shelx.scm group-settings.scm fitting.scm americanisms.scm tips.scm tips-gui.scm generic-objects.scm cns2coot.scm extensions.scm ncs.scm create-server.scsh coot-crash-catcher.scm '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/scheme'
 install -p -m 644 snarf-coot-docs.scm clear-backup.scm bones-reader.scm matrices.scm fascinating-things.scm shelx-extensions.scm parse-pisa-xml.scm check-for-updates.scm prodrg-import.scm get-recent-pdbe.scm json-reader.scm jligand.scm jligand-gui.scm redefine-functions.scm user-define-restraints.scm '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/scheme'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/scheme'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/scheme'
Making install in python
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/python'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/python'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python'
 install -p -m 644 coot_utils.py get_ebi.py mutate.py background_demo.py hello.py raster3d.py brute_lsqman.py refmac.py coot_gui.py filter.py libcheck.py coot_load_modules.py local_code.py gap.py remote_control.py povray.py coot_lsq.py shelx.py group_settings.py fitting.py americanisms.py tips.py tips_gui.py generic_objects.py cns2coot.py extensions.py ncs.py create_server.py python_coot_docs.py clear_backup.py bones_reader.py shelx_extensions.py parse_pisa_xml.py check_for_updates.py prodrg_import.py get_recent_pdbe.py jligand.py jligand_gui.py redefine_functions.py user_define_restraints.py '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python'
 install -p -m 644 coot_toolbuttons.py rcrane_loader.py '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/python'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/python'
Making install in pdb-templates
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
 install -p -m 644 ASN-NAG-via-NAG-ASN.pdb pyranose-pyranose-via-BETA1-4.pdb pyranose-pyranose-via-ALPHA1-2.pdb pyranose-pyranose-via-ALPHA1-3.pdb pyranose-pyranose-via-ALPHA1-6.pdb SIA-pyranose-via-ALPHA2-3.pdb theor-helix-70.pdb '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
Making install in macros
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/macros'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/macros'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/macros'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/macros'
Making install in compat
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/compat'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/compat'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-compat.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-compat.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-compat.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so.0 || { rm -f libcoot-compat.so.0 && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so || { rm -f libcoot-compat.so && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so; }; })
libtool: install: install -p .libs/libcoot-compat.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-compat.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 coot-getopt.h '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/compat'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/compat'
Making install in utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/utils'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/utils'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-utils.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so.0 || { rm -f libcoot-utils.so.0 && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so || { rm -f libcoot-utils.so && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so; }; })
libtool: install: install -p .libs/libcoot-utils.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-utils.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 coot-utils.hh coot-fasta.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/utils'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/utils'
Making install in protein_db
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/protein_db'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/protein_db'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-protein-db.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-protein-db.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-protein-db.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0 || { rm -f libcoot-protein-db.so.0 && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so || { rm -f libcoot-protein-db.so && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so; }; })
libtool: install: install -p .libs/libcoot-protein-db.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-protein-db.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 protein_db.h protein_db_utils.h rna_db.h '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/protein_db'
 install -p -m 644 protein.db '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/protein_db'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/protein_db'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/protein_db'
Making install in mini-mol
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/mini-mol'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/mini-mol'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-mini-mol.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-mini-mol.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-mini-mol.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0 || { rm -f libcoot-mini-mol.so.0 && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so || { rm -f libcoot-mini-mol.so && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so; }; })
libtool: install: install -p .libs/libcoot-mini-mol.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-mini-mol.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 mini-mol.hh mini-mol-utils.hh atom-quads.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/mini-mol'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/mini-mol'
Making install in geometry
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/geometry'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/geometry'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-geometry.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-geometry.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/geometry; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo chem_mods.lo lbg-graph.lo ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/lbg-graph.o   -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0
libtool: install: install -p .libs/libcoot-geometry.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-geometry.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so.0 || { rm -f libcoot-geometry.so.0 && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so || { rm -f libcoot-geometry.so && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so; }; })
libtool: install: install -p .libs/libcoot-geometry.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-geometry.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 protein-geometry.hh read-sbase.hh lbg-graph.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/geometry'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/geometry'
Making install in coot-utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-utils'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-utils'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-coord-utils.la libcoot-shelx.la libcoot-coord-extras.la libcoot-map-utils.la libcoot-map-heavy.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-coord-utils.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coot-utils; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-coord-utils.la -rpath /usr/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o .libs/coot-h-bonds.o .libs/hole.o .libs/read-sm-cif.o .libs/bonded-pairs.o .libs/helix-analysis.o .libs/elastic.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0
libtool: install: install -p .libs/libcoot-coord-utils.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0 || { rm -f libcoot-coord-utils.so.0 && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so || { rm -f libcoot-coord-utils.so && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so; }; })
libtool: install: install -p .libs/libcoot-coord-utils.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-utils.la
libtool: install: warning: relinking `libcoot-shelx.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coot-utils; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-shelx.la -rpath /usr/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-shelx-ins.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lcoot-utils -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0
libtool: install: install -p .libs/libcoot-shelx.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-shelx.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so.0 || { rm -f libcoot-shelx.so.0 && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so || { rm -f libcoot-shelx.so && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so; }; })
libtool: install: install -p .libs/libcoot-shelx.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-shelx.la
libtool: install: warning: relinking `libcoot-coord-extras.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coot-utils; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-coord-extras.la -rpath /usr/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o .libs/water-coordination.o .libs/lsq-improve.o .libs/coot-coord-utils-glyco.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lcoot-utils -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0
libtool: install: install -p .libs/libcoot-coord-extras.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-extras.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0 || { rm -f libcoot-coord-extras.so.0 && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so || { rm -f libcoot-coord-extras.so && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so; }; })
libtool: install: install -p .libs/libcoot-coord-extras.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-extras.la
libtool: install: warning: relinking `libcoot-map-utils.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coot-utils; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-map-utils.la -rpath /usr/lib coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo libcoot-coord-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-map-utils.o .libs/peak-search.o .libs/peak-search-from-list.o .libs/trim.o .libs/xmap-stats.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0
libtool: install: install -p .libs/libcoot-map-utils.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0 || { rm -f libcoot-map-utils.so.0 && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so || { rm -f libcoot-map-utils.so && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so; }; })
libtool: install: install -p .libs/libcoot-map-utils.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-utils.la
libtool: install: warning: relinking `libcoot-map-heavy.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coot-utils; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-map-heavy.la -rpath /usr/lib coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-map-heavy.o .libs/coot-fffear.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-map-utils -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lcoot-utils -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0
libtool: install: install -p .libs/libcoot-map-heavy.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-heavy.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0 || { rm -f libcoot-map-heavy.so.0 && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so || { rm -f libcoot-map-heavy.so && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so; }; })
libtool: install: install -p .libs/libcoot-map-heavy.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-heavy.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 peak-search.hh coot-trim.hh coot-coord-utils.hh coot-map-utils.hh coot-coord-extras.hh coot-map-heavy.hh coot-lsq-types.h coot-shelx.hh coot-rama.hh xmap-stats.hh coot-h-bonds.hh lsq-improve.hh coot-hole.hh read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-utils'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-utils'
Making install in surface
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/surface'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/surface'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libccp4mg-surface.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libccp4mg-surface.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-surface.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libccp4mg-surface.so.0.0.0 libccp4mg-surface.so.0 || { rm -f libccp4mg-surface.so.0 && ln -s libccp4mg-surface.so.0.0.0 libccp4mg-surface.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libccp4mg-surface.so.0.0.0 libccp4mg-surface.so || { rm -f libccp4mg-surface.so && ln -s libccp4mg-surface.so.0.0.0 libccp4mg-surface.so; }; })
libtool: install: install -p .libs/libccp4mg-surface.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-surface.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/surface'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/surface'
Making install in coot-surface
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-surface'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-surface'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-surface.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-surface.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coot-surface; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -lGL -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/coot-surface.o .libs/rgbreps.o   -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lccp4mg-surface -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lGL -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0
libtool: install: install -p .libs/libcoot-surface.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-surface.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so.0 || { rm -f libcoot-surface.so.0 && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so || { rm -f libcoot-surface.so && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so; }; })
libtool: install: install -p .libs/libcoot-surface.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-surface.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-surface'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-surface'
Making install in lidia-core
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/lidia-core'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/lidia-core'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-lidia-core.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-lidia-core.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/lidia-core; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-lidia-core.la -rpath /usr/lib lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/lbg-shared.o .libs/lbg-molfile.o .libs/lig-build.o .libs/rdkit-interface.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lcoot-utils -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0
libtool: install: install -p .libs/libcoot-lidia-core.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia-core.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0 || { rm -f libcoot-lidia-core.so.0 && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so || { rm -f libcoot-lidia-core.so && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so; }; })
libtool: install: install -p .libs/libcoot-lidia-core.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia-core.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 lbg-shared.hh lbg-molfile.hh lig-build.hh rdkit-interface.hh use-rdkit.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/lidia-core'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/lidia-core'
Making install in coords
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coords'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/coords'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-coords.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-coords.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/coords; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-shelx -lcoot-coord-utils -lcoot-lidia-core -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lcoot-utils -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0
libtool: install: install -p .libs/libcoot-coords.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coords.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so.0 || { rm -f libcoot-coords.so.0 && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so || { rm -f libcoot-coords.so && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so; }; })
libtool: install: install -p .libs/libcoot-coords.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coords.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 Bond_lines.h Cartesian.h cos-sin.h mmdb.h mmdb-extras.h utils.h mmdb-crystal.h Bond_lines_ext.h coot-close.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/coords'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coords'
Making install in angles
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/angles'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/angles'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-AngleInfo.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-AngleInfo.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-AngleInfo.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0 || { rm -f libcoot-AngleInfo.so.0 && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so || { rm -f libcoot-AngleInfo.so && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so; }; })
libtool: install: install -p .libs/libcoot-AngleInfo.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-AngleInfo.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 AngleInfo.h ncube.h wrapped-ncube.h '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/angles'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/angles'
Making install in skeleton
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/skeleton'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/skeleton'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-skeleton.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-skeleton.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/skeleton; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-AngleInfo -lcoot-coords -lcoot-shelx -lcoot-coord-utils -lcoot-lidia-core -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0
libtool: install: install -p .libs/libcoot-skeleton.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-skeleton.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0 || { rm -f libcoot-skeleton.so.0 && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so || { rm -f libcoot-skeleton.so && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so; }; })
libtool: install: install -p .libs/libcoot-skeleton.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-skeleton.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 graphical_skel.h dm-utils.h BuildCas.h '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/skeleton'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/skeleton'
Making install in ccp4mg-utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libccp4mg-utils.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libccp4mg-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0 || { rm -f libccp4mg-utils.so.0 && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so || { rm -f libccp4mg-utils.so && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so; }; })
libtool: install: install -p .libs/libccp4mg-utils.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-utils.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 geomutil.h mgtree.h cartesian.h matrix.h quat.h ppmutil.h '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
Making install in density-contour
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/density-contour'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/density-contour'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-isosurface.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-isosurface.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/density-contour; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-isosurface.la -rpath /usr/lib Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coords -lcoot-shelx -lcoot-coord-utils -lcoot-lidia-core -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0
libtool: install: install -p .libs/libcoot-isosurface.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-isosurface.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0 || { rm -f libcoot-isosurface.so.0 && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so || { rm -f libcoot-isosurface.so && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so; }; })
libtool: install: install -p .libs/libcoot-isosurface.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-isosurface.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 Vectors.h CIsoSurface.h density-contour-triangles.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/density-contour'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/density-contour'
Making install in db-main
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/db-main'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/db-main'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-db-main.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-db-main.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/db-main; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-db-main.la -rpath /usr/lib db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/db-main.o .libs/db-strands.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0
libtool: install: install -p .libs/libcoot-db-main.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-db-main.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so.0 || { rm -f libcoot-db-main.so.0 && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so || { rm -f libcoot-db-main.so && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so; }; })
libtool: install: install -p .libs/libcoot-db-main.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-db-main.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 db-main.hh db-strands.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/db-main'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/db-main'
Making install in ideal
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ideal'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/ideal'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-ideal.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-ideal.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/ideal; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -lgsl -lgslcblas -lm -lmmdb -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -Wl,-z,relro -o libcoot-ideal.la -rpath /usr/lib simple-restraint.lo chirals.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la -lgsl -lgslcblas -lm -lmmdb -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/simple-restraint.o .libs/chirals.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o .libs/torsion-bonds.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-coord-utils -lcoot-lidia-core -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lgsl -lgslcblas -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0
libtool: install: install -p .libs/libcoot-ideal.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ideal.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so.0 || { rm -f libcoot-ideal.so.0 && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so || { rm -f libcoot-ideal.so && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so; }; })
libtool: install: install -p .libs/libcoot-ideal.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ideal.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 test-indexing.hh simple-restraint.hh pepflip.hh regularize-minimol.hh lograma.h '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/ideal'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ideal'
Making install in ligand
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ligand'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/ligand'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-ligand.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-ligand.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/ligand; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-ligand.la -rpath /usr/lib ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o   -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/coords/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-ideal -lcoot-map-heavy -lgsl -lgslcblas -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-extras -lcoot-map-utils -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -fopenmp -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0
libtool: install: install -p .libs/libcoot-ligand.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ligand.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so.0 || { rm -f libcoot-ligand.so.0 && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so || { rm -f libcoot-ligand.so && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so; }; })
libtool: install: install -p .libs/libcoot-ligand.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ligand.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
  /bin/sh ../libtool   --mode=install install -p findligand-real findwaters-real '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
libtool: install: warning: `./libcoot-ligand.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/findligand-real /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/findligand-real
libtool: install: warning: `./libcoot-ligand.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/findwaters-real /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/findwaters-real
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
 install -p findwaters findligand '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh rigid-body.hh ideal-rna.hh rotamer.hh richardson-rotamer.hh torsion-general.hh primitive-chi-angles.hh dipole.hh base-pairing.hh backrub-rotamer.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/ligand'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ligand'
Making install in high-res
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/high-res'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/high-res'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-high-res.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-high-res.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/high-res; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o   -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/ideal/.libs -L/builddir/build/BUILD/coot-0.7/coot-utils/.libs -L/builddir/build/BUILD/coot-0.7/db-main/.libs -L/builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.7/coords/.libs -L/builddir/build/BUILD/coot-0.7/lidia-core/.libs -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-ligand -lcoot-ideal -lcoot-map-heavy -lgsl -lgslcblas -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-extras -lcoot-map-utils -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -fopenmp -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0
libtool: install: install -p .libs/libcoot-high-res.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-high-res.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so.0 || { rm -f libcoot-high-res.so.0 && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so || { rm -f libcoot-high-res.so && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so; }; })
libtool: install: install -p .libs/libcoot-high-res.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-high-res.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 high-res.hh coot-atom-graph.hh coot-node-info.hh sequence-assignment.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/high-res'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/high-res'
Making install in build
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/build'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/build'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-cabuild.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-cabuild.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/build; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-cabuild.la -rpath /usr/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/CalphaBuild.o   -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-AngleInfo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0
libtool: install: install -p .libs/libcoot-cabuild.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-cabuild.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0 || { rm -f libcoot-cabuild.so.0 && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so || { rm -f libcoot-cabuild.so && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so; }; })
libtool: install: install -p .libs/libcoot-cabuild.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-cabuild.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 CalphaBuild.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/build'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/build'
Making install in greg-tests
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/greg-tests'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/greg-tests'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/greg-tests'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/greg-tests'
Making install in python-tests
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/python-tests'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/python-tests'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/python-tests'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/python-tests'
Making install in analysis
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/analysis'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/analysis'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-analysis.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-analysis.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/analysis; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-analysis.la -rpath /usr/lib bfkurt.lo mogul.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/bfkurt.o .libs/mogul.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lcoot-utils -lmmdb -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0
libtool: install: install -p .libs/libcoot-analysis.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-analysis.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so.0 || { rm -f libcoot-analysis.so.0 && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so || { rm -f libcoot-analysis.so && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so; }; })
libtool: install: install -p .libs/libcoot-analysis.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-analysis.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
  /bin/sh ../libtool   --mode=install install -p bfactan '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
libtool: install: warning: `libcoot-analysis.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/bfactan /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/bfactan
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 bfkurt.hh mogul-interface.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/analysis'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/analysis'
Making install in tw
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/tw'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/tw'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-tw.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-tw.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-tw.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so.0 || { rm -f libcoot-tw.so.0 && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so || { rm -f libcoot-tw.so && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so; }; })
libtool: install: install -p .libs/libcoot-tw.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-tw.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 coot-tw.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/tw'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/tw'
Making install in libgtkgraph
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-gtkgraph.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcoot-gtkgraph.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-gtkgraph.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0 || { rm -f libcoot-gtkgraph.so.0 && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so || { rm -f libcoot-gtkgraph.so && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so; }; })
libtool: install: install -p .libs/libcoot-gtkgraph.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-gtkgraph.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
Making install in lbg
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/lbg'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/lbg'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-lidia.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-lidia.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/lbg; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-lidia.la -rpath /usr/lib lbg.lo wmolecule.lo lbg-search.lo residue-circles.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb -lmmdb -lgsl -lgslcblas -lm -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/lbg.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-lidia-core -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0
libtool: install: install -p .libs/libcoot-lidia.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so.0 || { rm -f libcoot-lidia.so.0 && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so || { rm -f libcoot-lidia.so && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so; }; })
libtool: install: install -p .libs/libcoot-lidia.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
  /bin/sh ../libtool   --mode=install install -p lidia '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
libtool: install: warning: `./libcoot-lidia.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/lidia /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/lidia
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/pixmaps'
 install -p -m 644 3-c-new.svg 6-c-shadow-experiment.svg single.svg 3-c-other.svg 6-c.svg sp3.svg 3-c.svg 7-c.svg stereo-out.svg 4-c.svg 8-c.svg TheStructorr_magnifying_glass-32.svg 5-c.svg Anonymous_Architetto_--_Chiave.svg TheStructorr_magnifying_glass.svg 6-c-arom.svg charge.svg triple.svg 6-c-exp-2.svg double.svg Trash-hydrogens-Andy_Trash_Can.svg face-smile.svg 05_Hotel_Icon_Hair_Salon.svg '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/pixmaps'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 install -p -m 644 lbg.hh wmolecule.hh flev-annotations.hh graphics-c-interface-functions.hh lbg-drag-and-drop.hh qed-interface.hh alerts.hh '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
 install -p -m 644 lbg.glade lbg-callbacks.cc '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/lbg'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/lbg'
Making install in cootaneer
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/cootaneer'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/cootaneer'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcootaneer.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcootaneer.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootaneer.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so.0 || { rm -f libcootaneer.so.0 && ln -s libcootaneer.so.0.0.0 libcootaneer.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so || { rm -f libcootaneer.so && ln -s libcootaneer.so.0.0.0 libcootaneer.so; }; })
libtool: install: install -p .libs/libcootaneer.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootaneer.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
 install -p -m 644 cootaneer-llk-2.40.dat '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootaneer'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootaneer'
Making install in cootilus
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/cootilus'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/cootilus'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcootilus.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: install -p .libs/libcootilus.so.0.0.0 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootilus.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcootilus.so.0.0.0 libcootilus.so.0 || { rm -f libcootilus.so.0 && ln -s libcootilus.so.0.0.0 libcootilus.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcootilus.so.0.0.0 libcootilus.so || { rm -f libcootilus.so && ln -s libcootilus.so.0.0.0 libcootilus.so; }; })
libtool: install: install -p .libs/libcootilus.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootilus.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
 install -p -m 644 nautilus_lib.pdb '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootilus'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootilus'
Making install in goograph
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/goograph'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/goograph'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
 /bin/sh ../libtool   --mode=install install -p   libcoot-goograph.la '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib'
libtool: install: warning: relinking `libcoot-goograph.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.7/goograph; /bin/sh /builddir/build/BUILD/coot-0.7/libtool  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z,relro -o libcoot-goograph.la -rpath /usr/lib goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386)
libtool: relink: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crti.o /usr/lib/gcc/i686-redhat-linux/4.8.1/crtbeginS.o  .libs/goograph.o   -L/builddir/build/BUILD/coot-0.7/geometry/.libs -L/builddir/build/BUILD/coot-0.7/mini-mol/.libs -L/builddir/build/BUILD/coot-0.7/utils/.libs -L/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib -L/usr/lib -lcoot-lidia-core -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lcoot-utils -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -L/usr/lib/gcc/i686-redhat-linux/4.8.1 -L/usr/lib/gcc/i686-redhat-linux/4.8.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/4.8.1/crtendS.o /usr/lib/gcc/i686-redhat-linux/4.8.1/../../../crtn.o  -O2 -m32 -march=i686 -mtune=atom -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0
libtool: install: install -p .libs/libcoot-goograph.so.0.0.0T /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-goograph.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so.0 || { rm -f libcoot-goograph.so.0 && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so || { rm -f libcoot-goograph.so && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so; }; })
libtool: install: install -p .libs/libcoot-goograph.lai /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-goograph.la
libtool: install: warning: remember to run `libtool --finish /usr/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/goograph'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/goograph'
Making install in src
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/src'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/src'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
  /bin/sh ../libtool   --mode=install install -p coot-real density-score-by-residue-real fix-nomenclature-errors '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
libtool: install: warning: `../lbg/libcoot-lidia.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ligand/libcoot-ligand.la' has not been installed in `/usr/lib'
libtool: install: warning: `../lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../goograph/libcoot-goograph.la' has not been installed in `/usr/lib'
libtool: install: warning: `../libgtkgraph/libcoot-gtkgraph.la' has not been installed in `/usr/lib'
libtool: install: warning: `../density-contour/libcoot-isosurface.la' has not been installed in `/usr/lib'
libtool: install: warning: `../build/libcoot-cabuild.la' has not been installed in `/usr/lib'
libtool: install: warning: `../skeleton/libcoot-skeleton.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/angles/libcoot-AngleInfo.la' has not been installed in `/usr/lib'
libtool: install: warning: `../angles/libcoot-AngleInfo.la' has not been installed in `/usr/lib'
libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `../high-res/libcoot-high-res.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ligand/libcoot-ligand.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-surface/libcoot-surface.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/surface/libccp4mg-surface.la' has not been installed in `/usr/lib'
libtool: install: warning: `../surface/libccp4mg-surface.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `../analysis/libcoot-analysis.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../protein_db/libcoot-protein-db.la' has not been installed in `/usr/lib'
libtool: install: warning: `../cootilus/libcootilus.la' has not been installed in `/usr/lib'
libtool: install: warning: `../cootaneer/libcootaneer.la' has not been installed in `/usr/lib'
libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/coot-real /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/coot-real
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../compat/libcoot-compat.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/density-score-by-residue-real /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/density-score-by-residue-real
libtool: install: warning: `../ligand/libcoot-ligand.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../db-main/libcoot-db-main.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ideal/libcoot-ideal.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-heavy.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coords/libcoot-coords.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `../ccp4mg-utils/libccp4mg-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-extras.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-map-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../coot-utils/libcoot-shelx.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/coot-utils/libcoot-coord-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../lidia-core/libcoot-lidia-core.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/geometry/libcoot-geometry.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: warning: `/builddir/build/BUILD/coot-0.7/utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../utils/libcoot-utils.la' has not been installed in `/usr/lib'
libtool: install: warning: `../mini-mol/libcoot-mini-mol.la' has not been installed in `/usr/lib'
libtool: install: install -p .libs/fix-nomenclature-errors /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/fix-nomenclature-errors
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
 install -p coot density-score-by-residue '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python'
 install -p coot.py '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/src'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/src'
Making install in data
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/data'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/data'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/data'
 install -p -m 644 tutorial-modern.pdb rnasa-1.8-all_refmac1.mtz '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/data'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/data'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/data'
Making install in rama-data
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/rama-data'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/rama-data'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/rama-data'
 install -p -m 644 rota500-arg.data rota500-asn.data rota500-asp.data rota500-cys.data rota500-gln.data rota500-glu.data rota500-his.data rota500-ile.data rota500-leu.data rota500-lys.data rota500-met.data rota500-phetyr.data rota500-pro.data rota500-ser.data rota500-thr.data rota500-trp.data rota500-val.data '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/rama-data'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/rama-data'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/rama-data'
Making install in doc
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/doc'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/doc'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/doc'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/doc'
Making install in rcrane
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/rcrane'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/rcrane'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane'
 install -p -m 644 CHANGELOG.txt buildPhosOxy.py installRCrane.py pseudoMolecule.py selectMapDialog.py LICENSE.txt calcCoords.py launch.py pseudoPredictor.py settings.py chain.py linearInterp.py puckerList.py smoothProb.py NOTICE.txt citationPopup.py logo.svg reviewSuitesGui.py stats.py README.txt coot_gui_adapter.py menu.py revisionNum.py strucCalc.py __init__.py coot_utils_adapter.py nextPhos.py rotData.py suite.py about.py nucleotide.py rotamerSeq.py thetaEtaPredictor.py bondLength.py guiUtils.py phenixRestraints.py rotamerize.py traceGui.py buildInitSugar.py icon.svg '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane'
 install -p -m 644 preLaunchCheck.py safelog.py extendChain.py reportInputErrors.py '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane/data'
 install -p -m 644 data/bases.pdb data/phosAngleSmoothed.csv data/sugarDists.csv data/c2p.pdb data/phosDistSmoothed.csv data/sugarPhosSugarAngleSmoothed.csv data/c3p.pdb data/pseudoChiSmoothed.csv data/thetaEtaClusts.csv data/dihedData.csv data/smoothedPuckerDist.csv data/endingPDists.csv data/startingPDists.csv '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane/data'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/rcrane'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/rcrane'
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7'
make[2]: Nothing to be done for `install-exec-am'.
if test -d ./pixmaps; then \
  /bin/sh ./mkinstalldirs /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/pixmaps; \
  for pixmap in ./pixmaps/*; do \
    if test -f $pixmap; then \
      install -p -m 644 $pixmap /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/pixmaps; \
    fi \
  done \
fi
if test -z "" ; then \
  install -p -m 644 ./syminfo.lib /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot; \
  else \
  install -p -m 644 ./windows/syminfo.lib /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot; \
fi
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
 install -p -m 644 cootrc standard-residues.pdb colours.def mtrix-to-ncs-matrix.awk '/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7'
+ mv reference-structures /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/
+ sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=/usr/lib/python2.7/site-packages/coot|' src/coot
+ sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=/usr/share/refmac-dictionary-5.41|' src/coot
+ install -p -m 755 src/coot /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/
+ rm -f /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-surface.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-utils.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-AngleInfo.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-analysis.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-cabuild.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-compat.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-extras.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-utils.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coords.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-db-main.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-geometry.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-goograph.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-gtkgraph.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-high-res.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ideal.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-isosurface.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia-core.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ligand.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-heavy.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-utils.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-mini-mol.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-protein-db.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-shelx.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-skeleton.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-surface.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-tw.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-utils.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootaneer.la /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootilus.la
+ mkdir /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/AngleInfo.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/Bond_lines.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/Bond_lines_ext.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/BuildCas.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/CIsoSurface.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/Cartesian.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/Vectors.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/cartesian.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-getopt.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-lsq-types.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/cos-sin.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/dm-utils.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/geomutil.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/graphical_skel.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lograma.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/matrix.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mgtree.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mmdb-crystal.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mmdb-extras.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mmdb.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/ncube.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/ppmutil.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/protein_db.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/protein_db_utils.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/quat.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/rna_db.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/utils.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/wrapped-ncube.h /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot/
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/CalphaBuild.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/alerts.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/atom-quads.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/backrub-rotamer.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/base-pairing.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/bfkurt.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/bonded-pairs.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/chi-angles.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-atom-graph.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-close.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-coord-extras.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-coord-utils.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-fasta.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-h-bonds.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-hole.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-map-heavy.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-map-utils.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-node-info.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-rama.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-shelx.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-trim.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-tw.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot-utils.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/db-main.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/db-strands.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/density-contour-triangles.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/dipole.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/dunbrack.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/elastic.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/fast-ss-search.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/flev-annotations.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/graphics-c-interface-functions.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/helix-analysis.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/helix-placement.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/high-res.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/ideal-rna.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lbg-drag-and-drop.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lbg-graph.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lbg-molfile.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lbg-shared.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lbg.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lig-build.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/ligand.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/lsq-improve.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mini-mol-utils.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mini-mol.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/mogul-interface.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/monomer-utils.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/peak-search.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/pepflip.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/primitive-chi-angles.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/protein-geometry.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/qed-interface.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/rdkit-interface.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/read-sbase.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/read-sm-cif.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/regularize-minimol.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/residue_by_phi_psi.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/richardson-rotamer.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/rigid-body.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/rotamer.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/sequence-assignment.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/simple-restraint.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/test-indexing.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/torsion-general.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/tree.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/use-rdkit.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/wligand.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/wmolecule.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/xmap-stats.hh /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/include/coot/
+ mkdir -p /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/americanisms.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/background_demo.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/bones_reader.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/brute_lsqman.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/check_for_updates.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/clear_backup.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/cns2coot.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/coot.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/coot_gui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/coot_load_modules.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/coot_lsq.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/coot_toolbuttons.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/coot_utils.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/create_server.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/extensions.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/filter.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/fitting.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/gap.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/generic_objects.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/get_ebi.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/get_recent_pdbe.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/group_settings.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/hello.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/jligand.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/jligand_gui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/libcheck.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/local_code.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/mutate.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/ncs.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/parse_pisa_xml.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/povray.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/prodrg_import.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/python_coot_docs.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/raster3d.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/rcrane_loader.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/redefine_functions.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/refmac.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/remote_control.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/shelx.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/shelx_extensions.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/tips.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/tips_gui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/coot/python/user_define_restraints.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/
++ find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name '*.py'
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/filter.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/filter.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/filter.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/filter.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/filter.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/jligand.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/povray.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/povray.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/povray.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/povray.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/povray.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/group_settings.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/group_settings.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/group_settings.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/group_settings.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/group_settings.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/prodrg_import.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/prodrg_import.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/prodrg_import.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/prodrg_import.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/prodrg_import.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/mutate.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/mutate.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/mutate.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/mutate.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/mutate.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/libcheck.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/libcheck.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/libcheck.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/libcheck.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/libcheck.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/gap.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/gap.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/gap.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/gap.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/gap.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ncs.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ncs.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ncs.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ncs.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ncs.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/local_code.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/local_code.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/local_code.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/local_code.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/local_code.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/tips.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/raster3d.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/raster3d.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/raster3d.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/raster3d.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/raster3d.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/background_demo.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/background_demo.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/background_demo.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/background_demo.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/background_demo.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/fitting.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/fitting.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/fitting.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/fitting.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/fitting.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/shelx.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/hello.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/hello.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/hello.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/hello.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/hello.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/remote_control.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/remote_control.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/remote_control.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/remote_control.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/remote_control.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/create_server.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/create_server.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/create_server.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/create_server.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/create_server.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/refmac.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/refmac.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/refmac.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/refmac.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/refmac.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/extensions.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/extensions.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/extensions.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/extensions.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/extensions.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/americanisms.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/americanisms.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/americanisms.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/americanisms.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/americanisms.py
+ for lib in '$(find /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py")'
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py
+ touch -r /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py.new
+ mv /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py.new /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py
+ cp /builddir/build/SOURCES/__init__.py /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/
+ chmod 644 /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/site-packages/coot/coot.py
+ desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/applications /builddir/build/SOURCES/coot.desktop
/builddir/build/SOURCES/coot.desktop: warning: key "Categories" is a list and does not have a semicolon as trailing character, fixing
+ mkdir -p /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/pixmaps
+ install -p -m 644 /builddir/build/SOURCES/coot.png /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/pixmaps/
+ /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/coot-0.7
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-surface.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ideal.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-lidia-core.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-gtkgraph.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-extras.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootaneer.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-surface.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-high-res.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcootilus.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-geometry.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-mini-mol.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-AngleInfo.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-goograph.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-protein-db.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-db-main.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-ligand.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-tw.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-skeleton.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-heavy.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coords.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-shelx.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libccp4mg-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-coord-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-map-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-analysis.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-isosurface.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-compat.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/libcoot-cabuild.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/density-score-by-residue-real
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/findwaters-real
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/findligand-real
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/bfactan
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/coot-real
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/lidia
extracting debug info from /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/bin/fix-nomenclature-errors
/usr/lib/rpm/sepdebugcrcfix: Updated 37 CRC32s, 0 CRC32s did match.
symlinked /usr/lib/debug/usr/lib/libcoot-cabuild.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-cabuild.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-map-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-map-utils.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-lidia-core.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-lidia-core.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-skeleton.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-skeleton.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-map-heavy.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-map-heavy.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-coords.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-coords.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-surface.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-surface.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-isosurface.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-isosurface.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-db-main.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-db-main.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-analysis.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-analysis.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-compat.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-compat.so.0.debug
symlinked /usr/lib/debug/usr/lib/libccp4mg-surface.so.0.0.0.debug to /usr/lib/debug/usr/lib/libccp4mg-surface.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-utils.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-ideal.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-ideal.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-geometry.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-geometry.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-tw.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-tw.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-ideal.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-ideal.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-compat.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-compat.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-goograph.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-goograph.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-shelx.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-shelx.so.debug
symlinked /usr/lib/debug/usr/lib/libccp4mg-surface.so.0.0.0.debug to /usr/lib/debug/usr/lib/libccp4mg-surface.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-mini-mol.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-mini-mol.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-geometry.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-geometry.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcootilus.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcootilus.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-mini-mol.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-mini-mol.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-coords.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-coords.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-cabuild.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-cabuild.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-AngleInfo.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-AngleInfo.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-ligand.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-ligand.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-goograph.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-goograph.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-lidia.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-lidia.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-map-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-map-utils.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-protein-db.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-protein-db.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-tw.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-tw.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-shelx.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-shelx.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-analysis.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-analysis.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-utils.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-gtkgraph.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-gtkgraph.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcootaneer.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcootaneer.so.0.debug
symlinked /usr/lib/debug/usr/lib/libccp4mg-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libccp4mg-utils.so.debug
symlinked /usr/lib/debug/usr/lib/libcootaneer.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcootaneer.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-AngleInfo.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-AngleInfo.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-skeleton.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-skeleton.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-map-heavy.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-map-heavy.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-protein-db.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-protein-db.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-ligand.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-ligand.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-isosurface.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-isosurface.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-coord-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-coord-utils.so.0.debug
symlinked /usr/lib/debug/usr/lib/libccp4mg-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libccp4mg-utils.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-lidia-core.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-lidia-core.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcootilus.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcootilus.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-coord-extras.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-coord-extras.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-high-res.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-high-res.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-coord-utils.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-coord-utils.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-surface.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-surface.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-gtkgraph.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-gtkgraph.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-db-main.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-db-main.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-lidia.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-lidia.so.debug
symlinked /usr/lib/debug/usr/lib/libcoot-high-res.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-high-res.so.0.debug
symlinked /usr/lib/debug/usr/lib/libcoot-coord-extras.so.0.0.0.debug to /usr/lib/debug/usr/lib/libcoot-coord-extras.so.0.debug
28956 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
Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/lib/python2.7/ using /usr/bin/python2.7
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.6MdoCD
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.7
+ make check
Making check in auxil
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
Making check in catcheck
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
make  catcheck
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o catcheck.o catcheck.cc
catcheck.cc: In function 'void water_coordination_check(CMMDBManager*, float)':
catcheck.cc:96:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<atom_contacts.size(); i++) {
                                       ^
catcheck.cc:127:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<atom_contacts.size(); i++) {
                                       ^
catcheck.cc:134:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<atom_contacts[i].contact_indices.size(); j++) {
                                                             ^
/bin/sh ../../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o catcheck catcheck.o -lmmdb   
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o catcheck catcheck.o  -lmmdb
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/catcheck'
Making check in rama
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
make  rama-data rama-doughnut
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rama-data.o rama-data.cc
rama-data.cc: In function 'int main(int, char**)':
rama-data.cc:16:11: warning: unused variable 'phi' [-Wunused-variable]
    double phi = -57;
           ^
rama-data.cc:17:11: warning: unused variable 'psi' [-Wunused-variable]
    double psi = -48;
           ^
/bin/sh ../../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o rama-data rama-data.o -lmmdb  	-lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb    
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o rama-data rama-data.o  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o rama-doughnut.o rama-doughnut.cc
rama-doughnut.cc: In function 'int main(int, char**)':
rama-doughnut.cc:16:11: warning: unused variable 'phi' [-Wunused-variable]
    double phi = -57;
           ^
rama-doughnut.cc:17:11: warning: unused variable 'psi' [-Wunused-variable]
    double psi = -48;
           ^
/bin/sh ../../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o rama-doughnut rama-doughnut.o -lmmdb   -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb    
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o rama-doughnut rama-doughnut.o  -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/rama'
Making check in sec-str
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/sec-str'
Making check in strand-analysis
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make  
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/strand-analysis'
Making check in vectors
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make  
make[3]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil/vectors'
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/auxil'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/auxil'
Making check in scheme
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/scheme'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/scheme'
Making check in python
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/python'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/python'
Making check in pdb-templates
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/pdb-templates'
Making check in macros
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/macros'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/macros'
Making check in compat
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/compat'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/compat'
Making check in utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/utils'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/utils'
Making check in protein_db
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/protein_db'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/protein_db'
Making check in mini-mol
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/mini-mol'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/mini-mol'
Making check in geometry
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/geometry'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/geometry'
Making check in coot-utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-utils'
make  test-tt-morph
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-utils'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP   -I/usr/include -DUSE_GUILE -DUSE_PYTHON  -I/usr/include/mmdb -I/usr/include/ssm -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-morph.o test-morph.cc
In file included from coot-map-utils.hh:29:0,
                 from test-morph.cc:6:
coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
test-morph.cc: In function 'clipper::Coord_orth get_coords_centre(const std::vector<coot::residue_spec_t>&, CMMDBManager*)':
test-morph.cc:21:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (unsigned int iat=0; iat<n_residue_atoms; iat++) {
                                ^
test-morph.cc: In function 'int main(int, char**)':
test-morph.cc:61:8: warning: unused variable 'r' [-Wunused-variable]
   bool r = coot::util::map_fill_from_mtz(&xmap, mtz_file_name, f_col, phi_col, "", 0, 0);
        ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-tt-morph test-morph.o ./libcoot-map-heavy.la 
libtool: link: g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-tt-morph test-morph.o  ./.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lgsl -lgslcblas
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-utils'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-utils'
Making check in surface
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/surface'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/surface'
Making check in coot-surface
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coot-surface'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coot-surface'
Making check in lidia-core
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/lidia-core'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/lidia-core'
Making check in coords
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/coords'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/coords'
Making check in angles
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/angles'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/angles'
Making check in skeleton
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/skeleton'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/skeleton'
Making check in ccp4mg-utils
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ccp4mg-utils'
Making check in density-contour
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/density-contour'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/density-contour'
Making check in db-main
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/db-main'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/db-main'
Making check in ideal
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ideal'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ideal'
Making check in ligand
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/ligand'
make  test-fffear-in-coot
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/ligand'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP     -I/usr/include/mmdb -I/usr/include/ssm -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-fffear-in-coot.o test-fffear-in-coot.cc
In file included from ../lidia-core/lbg-molfile.hh:32:0,
                 from ../coords/mmdb.h:25,
                 from test-fffear-in-coot.cc:44:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from ../coot-utils/coot-map-utils.hh:29:0,
                 from test-fffear-in-coot.cc:47:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
test-fffear-in-coot.cc: In function 'int main(int, char**)':
test-fffear-in-coot.cc:171:17: warning: variable 'do_it_with_map' set but not used [-Wunused-but-set-variable]
       short int do_it_with_map = 0;
                 ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -fopenmp -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-fffear-in-coot test-fffear-in-coot.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-coord-extras.la ../coords/libcoot-coords.la ../coot-utils/libcoot-shelx.la ../geometry/libcoot-geometry.la ../coot-utils/libcoot-map-heavy.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../ccp4mg-utils/libccp4mg-utils.la ../compat/libcoot-compat.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb   -lmmdb   -lgsl -lgslcblas -lm 
libtool: link: g++ -fopenmp -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-fffear-in-coot test-fffear-in-coot.o  ./.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.7/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.7/ccp4mg-utils/.libs/libccp4mg-utils.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-extras.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-shelx.so ../geometry/.libs/libcoot-geometry.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-map-utils.so ../db-main/.libs/libcoot-db-main.so ../coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb -lgsl -lgslcblas -lm -fopenmp
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/ligand'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/ligand'
Making check in high-res
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/high-res'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/high-res'
Making check in build
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/build'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/build'
Making check in greg-tests
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/greg-tests'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/greg-tests'
Making check in python-tests
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/python-tests'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/python-tests'
Making check in analysis
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/analysis'
make  test-mogul
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/analysis'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coot-utils -I../mini-mol -I../utils  -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-mogul.o test-mogul.cc
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-mogul test-mogul.o libcoot-analysis.la 
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-mogul test-mogul.o  ./.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lmmdb
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/analysis'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/analysis'
Making check in tw
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/tw'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/tw'
Making check in libgtkgraph
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/libgtkgraph'
Making check in lbg
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/lbg'
make  test_lbg_functions
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/lbg'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test_lbg_functions.o test_lbg_functions.cc
In file included from /usr/include/python2.7/pyconfig.h:4:0,
                 from /usr/include/python2.7/Python.h:8,
                 from lbg.hh:31,
                 from test_lbg_functions.cc:25:
/usr/include/python2.7/pyconfig-32.h:1182:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/limits.h:26:0,
                 from /usr/lib/gcc/i686-redhat-linux/4.8.1/include/limits.h:168,
                 from /usr/lib/gcc/i686-redhat-linux/4.8.1/include/syslimits.h:7,
                 from /usr/lib/gcc/i686-redhat-linux/4.8.1/include/limits.h:34,
                 from /usr/lib/glib-2.0/include/glibconfig.h:11,
                 from /usr/include/glib-2.0/glib/gtypes.h:34,
                 from /usr/include/glib-2.0/glib/galloca.h:34,
                 from /usr/include/glib-2.0/glib.h:32,
                 from /usr/include/glib-2.0/gobject/gbinding.h:30,
                 from /usr/include/glib-2.0/glib-object.h:25,
                 from /usr/include/glib-2.0/gio/gioenums.h:30,
                 from /usr/include/glib-2.0/gio/giotypes.h:30,
                 from /usr/include/glib-2.0/gio/gio.h:28,
                 from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
                 from /usr/include/gtk-2.0/gdk/gdk.h:32,
                 from /usr/include/gtk-2.0/gtk/gtk.h:32,
                 from /usr/include/goocanvas-1.0/goocanvas.h:10,
                 from test_lbg_functions.cc:21:
/usr/include/features.h:168:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
In file included from /usr/include/python2.7/pyconfig.h:4:0,
                 from /usr/include/python2.7/Python.h:8,
                 from lbg.hh:31,
                 from test_lbg_functions.cc:25:
/usr/include/python2.7/pyconfig-32.h:1204:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
 #define _XOPEN_SOURCE 600
 ^
In file included from /usr/include/limits.h:26:0,
                 from /usr/lib/gcc/i686-redhat-linux/4.8.1/include/limits.h:168,
                 from /usr/lib/gcc/i686-redhat-linux/4.8.1/include/syslimits.h:7,
                 from /usr/lib/gcc/i686-redhat-linux/4.8.1/include/limits.h:34,
                 from /usr/lib/glib-2.0/include/glibconfig.h:11,
                 from /usr/include/glib-2.0/glib/gtypes.h:34,
                 from /usr/include/glib-2.0/glib/galloca.h:34,
                 from /usr/include/glib-2.0/glib.h:32,
                 from /usr/include/glib-2.0/gobject/gbinding.h:30,
                 from /usr/include/glib-2.0/glib-object.h:25,
                 from /usr/include/glib-2.0/gio/gioenums.h:30,
                 from /usr/include/glib-2.0/gio/giotypes.h:30,
                 from /usr/include/glib-2.0/gio/gio.h:28,
                 from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
                 from /usr/include/gtk-2.0/gdk/gdk.h:32,
                 from /usr/include/gtk-2.0/gtk/gtk.h:32,
                 from /usr/include/goocanvas-1.0/goocanvas.h:10,
                 from test_lbg_functions.cc:21:
/usr/include/features.h:170:0: note: this is the location of the previous definition
 # define _XOPEN_SOURCE 700
 ^
In file included from lbg.hh:53:0,
                 from test_lbg_functions.cc:25:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from lbg.hh:61:0,
                 from test_lbg_functions.cc:25:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz    -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP      -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -I/usr/include/mmdb -I/usr/include/ssm -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o graphics-c-interface-functions-blanks.o graphics-c-interface-functions-blanks.cc
In file included from graphics-c-interface-functions-blanks.cc:2:0:
../coot-utils/coot-coord-utils.hh: In member function 'bool coot::util::contact_atoms_info_t::has_contacts(int, double) const':
../coot-utils/coot-coord-utils.hh:1064:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (size() >= n_contacts) {
                    ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test_lbg_functions test_lbg_functions.o graphics-c-interface-functions-blanks.o ./libcoot-lidia.la ../lidia-core/libcoot-lidia-core.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -lutil  
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test_lbg_functions test_lbg_functions.o graphics-c-interface-functions-blanks.o -Wl,-export-dynamic  ./.libs/libcoot-lidia.so /builddir/build/BUILD/coot-0.7/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so -lgsl -lgslcblas -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb ../utils/.libs/libcoot-utils.so -lpthread -ldl -lm -lpython2.7 -lutil
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/lbg'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/lbg'
Making check in cootaneer
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/cootaneer'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootaneer'
Making check in cootilus
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/cootilus'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/cootilus'
Making check in goograph
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/goograph'
make  test-goograph
make[2]: Entering directory `/builddir/build/BUILD/coot-0.7/goograph'
g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../utils -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/harfbuzz            -I/usr/include/mmdb -I/usr/include/ssm  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -c -o test-goograph.o test-goograph.cc
In file included from goograph.hh:32:0,
                 from test-goograph.cc:22:
../lidia-core/lig-build.hh: In member function 'bool lig_build::pos_t::close_point(const lig_build::pos_t&) const':
../lidia-core/lig-build.hh:75:8: warning: unused variable 'status' [-Wunused-variable]
   bool status = 0;
        ^
../lidia-core/lig-build.hh: In member function 'lig_build::pos_t lig_build::pos_t::rotate_about(double, double, double)':
../lidia-core/lig-build.hh:114:10: warning: unused variable 'delta_x' [-Wunused-variable]
   double delta_x = x - x_cen;
          ^
../lidia-core/lig-build.hh:115:10: warning: unused variable 'delta_y' [-Wunused-variable]
   double delta_y = y - y_cen;
          ^
In file included from test-goograph.cc:22:0:
goograph.hh: In member function 'bool coot::goograph::is_valid_trace(int)':
goograph.hh:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if (trace_id >= traces.size()) {
                                  ^
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches  -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing  -Wl,-z,relro  -o test-goograph test-goograph.o libcoot-goograph.la ../utils/libcoot-utils.la 
libtool: link: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fno-strict-aliasing -Wl,-z -Wl,relro -o .libs/test-goograph test-goograph.o  ./.libs/libcoot-goograph.so /builddir/build/BUILD/coot-0.7/lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.7/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.7/mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb /builddir/build/BUILD/coot-0.7/utils/.libs/libcoot-utils.so -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 ../utils/.libs/libcoot-utils.so
make[2]: Leaving directory `/builddir/build/BUILD/coot-0.7/goograph'
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/goograph'
Making check in src
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/src'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/src'
Making check in data
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/data'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/data'
Making check in rama-data
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/rama-data'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/rama-data'
Making check in doc
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/doc'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/doc'
Making check in rcrane
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7/rcrane'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7/rcrane'
make[1]: Entering directory `/builddir/build/BUILD/coot-0.7'
make[1]: Nothing to be done for `check-am'.
make[1]: Leaving directory `/builddir/build/BUILD/coot-0.7'
+ exit 0
Processing files: coot-0.7-5.20120929svn4458.fc19.i686
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FFXeyJ
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.7
+ DOCDIR=/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-0.7
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-0.7
+ cp -pr AUTHORS /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-0.7
+ cp -pr README /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-0.7
+ cp -pr COPYING /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-0.7
+ exit 0
Provides: coot = 0.7-5.20120929svn4458.fc19 coot(x86-32) = 0.7-5.20120929svn4458.fc19 libccp4mg-surface.so.0 libccp4mg-utils.so.0 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-cabuild.so.0 libcoot-compat.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-geometry.so.0 libcoot-goograph.so.0 libcoot-gtkgraph.so.0 libcoot-high-res.so.0 libcoot-ideal.so.0 libcoot-isosurface.so.0 libcoot-lidia-core.so.0 libcoot-lidia.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-protein-db.so.0 libcoot-shelx.so.0 libcoot-skeleton.so.0 libcoot-surface.so.0 libcoot-tw.so.0 libcoot-utils.so.0 libcootaneer.so.0 libcootilus.so.0
Requires(interp): /sbin/ldconfig /sbin/ldconfig
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /sbin/ldconfig
Requires(postun): /sbin/ldconfig
Requires: /bin/sh libGL.so.1 libGLU.so.1 libICE.so.6 libSM.so.6 libX11.so.6 libXmu.so.6 libXt.so.6 libart_lgpl_2.so.2 libatk-1.0.so.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.11) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libcairo.so.2 libccp4c.so.0 libccp4mg-surface.so.0 libccp4mg-utils.so.0 libclipper-ccp4.so.2 libclipper-cif.so.2 libclipper-cns.so.2 libclipper-contrib.so.2 libclipper-core.so.2 libclipper-fortran.so.2 libclipper-minimol.so.2 libclipper-mmdb.so.2 libclipper-phs.so.2 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-cabuild.so.0 libcoot-compat.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-geometry.so.0 libcoot-goograph.so.0 libcoot-gtkgraph.so.0 libcoot-high-res.so.0 libcoot-ideal.so.0 libcoot-isosurface.so.0 libcoot-lidia-core.so.0 libcoot-lidia.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-protein-db.so.0 libcoot-shelx.so.0 libcoot-skeleton.so.0 libcoot-surface.so.0 libcoot-utils.so.0 libcootaneer.so.0 libcootilus.so.0 libcurl.so.4 libdl.so.2 libfontconfig.so.1 libfreetype.so.6 libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgdk-x11-2.0.so.0 libgdk_pixbuf-2.0.so.0 libgdkglext-x11-1.0.so.0 libgio-2.0.so.0 libglib-2.0.so.0 libglut.so.3 libgmodule-2.0.so.0 libgnomecanvas-2.so.0 libgobject-2.0.so.0 libgomp.so.1 libgomp.so.1(GOMP_1.0) libgoocanvas.so.3 libgsl.so.0 libgslcblas.so.0 libgtk-x11-2.0.so.0 libgtkglext-x11-1.0.so.0 libguile.so.17 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libmmdb.so.0 libpango-1.0.so.0 libpangocairo-1.0.so.0 libpangoft2-1.0.so.0 libpangox-1.0.so.0 libpng15.so.15 libpng15.so.15(PNG15_0) libpthread.so.0 libpthread.so.0(GLIBC_2.0) libpython2.7.so.1.0 libsfftw.so.2 libsrfftw.so.2 libssm.so.1 libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.1) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.9) libutil.so.1 python(abi) = 2.7 rtld(GNU_HASH)
Processing files: coot-devel-0.7-5.20120929svn4458.fc19.i686
Provides: coot-devel = 0.7-5.20120929svn4458.fc19 coot-devel(x86-32) = 0.7-5.20120929svn4458.fc19
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libccp4mg-surface.so.0 libccp4mg-utils.so.0 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-cabuild.so.0 libcoot-compat.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-geometry.so.0 libcoot-goograph.so.0 libcoot-gtkgraph.so.0 libcoot-high-res.so.0 libcoot-ideal.so.0 libcoot-isosurface.so.0 libcoot-lidia-core.so.0 libcoot-lidia.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-protein-db.so.0 libcoot-shelx.so.0 libcoot-skeleton.so.0 libcoot-surface.so.0 libcoot-tw.so.0 libcoot-utils.so.0 libcootaneer.so.0 libcootilus.so.0
Processing files: coot-doc-0.7-5.20120929svn4458.fc19.i686
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.6YNb3e
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.7
+ DOCDIR=/builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-doc-0.7
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-doc-0.7
+ cp -pr doc/coot-keys-and-buttons.pdf /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-doc-0.7
+ cp -pr doc/coot-user-manual.pdf /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386/usr/share/doc/coot-doc-0.7
+ exit 0
Provides: coot-doc = 0.7-5.20120929svn4458.fc19 coot-doc(x86-32) = 0.7-5.20120929svn4458.fc19
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: coot-debuginfo-0.7-5.20120929svn4458.fc19.i686
Provides: coot-debuginfo = 0.7-5.20120929svn4458.fc19 coot-debuginfo(x86-32) = 0.7-5.20120929svn4458.fc19
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/coot-0.7-5.20120929svn4458.fc19.i386
Wrote: /builddir/build/RPMS/coot-0.7-5.20120929svn4458.fc19.i686.rpm
Wrote: /builddir/build/RPMS/coot-devel-0.7-5.20120929svn4458.fc19.i686.rpm
Wrote: /builddir/build/RPMS/coot-doc-0.7-5.20120929svn4458.fc19.i686.rpm
Wrote: /builddir/build/RPMS/coot-debuginfo-0.7-5.20120929svn4458.fc19.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.fMw1LJ
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.7
+ rm -rf /builddir/build/BUILDROOT/coot-0.7-5.20120929svn4458.fc19.i386
+ exit 0
Child return code was: 0
LEAVE do -->