Mock Version: 1.4.2
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/coot.spec'], chrootPath='/var/lib/mock/579072-fedora-rawhide-x86_64/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f659ce8d080>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--private-network']printOutput=True)
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'd9a3e97b43794d4fb4ac070b728930f8', '-D', '/var/lib/mock/579072-fedora-rawhide-x86_64/root', '-a', '--private-network', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/coot.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/coot-0.8.8-2.fc27.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/coot.spec'], chrootPath='/var/lib/mock/579072-fedora-rawhide-x86_64/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f659ce8d080>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--private-network', '--private-network']printOutput=True)
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '5e7e6e39a0794189a68d5e813d6f8d72', '-D', '/var/lib/mock/579072-fedora-rawhide-x86_64/root', '-a', '--private-network', '--private-network', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/coot.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.qIAn8I
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf coot-0.8.8
+ /usr/bin/gzip -dc /builddir/build/SOURCES/coot-0.8.8.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd coot-0.8.8
+ /usr/bin/tar -xof -
+ /usr/bin/gzip -dc /builddir/build/SOURCES/reference-structures.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (coot-configure.ac.patch):
+ echo 'Patch #0 (coot-configure.ac.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0
patching file configure.ac
Hunk #2 succeeded at 157 (offset 9 lines).
Patch #1 (coot-makefile.patch):
+ echo 'Patch #1 (coot-makefile.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0
patching file src/Makefile.am
Hunk #1 succeeded at 460 (offset 3 lines).
patching file lbg/Makefile.am
Patch #2 (coot-guile.patch):
+ echo 'Patch #2 (coot-guile.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0
patching file macros/guile.m4
Patch #3 (coot-utils.patch):
+ echo 'Patch #3 (coot-utils.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0
patching file coot-utils/coot-shelx.hh
patching file coot-utils/coot-hole.hh
Patch #4 (coot-rdkit.patch):
+ echo 'Patch #4 (coot-rdkit.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0
patching file lbg/lbg-search.cc
Patch #5 (coot-lbg.patch):
+ echo 'Patch #5 (coot-lbg.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0
patching file lbg/lbg.cc
Hunk #1 succeeded at 4905 (offset 32 lines).
+ cp /builddir/build/SOURCES/coot.in ./src/
+ cp /builddir/build/SOURCES/coot.desktop .
+ iconv -f iso8859-1 -t utf-8 README
+ mv -f README.conv README
+ rm macros/libtool.m4
+ aclocal -I macros
+ libtoolize --automake --copy
+ autoconf
+ automake --copy --add-missing --gnu
src/Makefile.am:464: warning: pythondir was already defined in condition TRUE, which includes condition COOT_USE_PYTHON ...
configure.ac:215: ... 'pythondir' previously defined here
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.GigI4x
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.8.8
+ mkdir guile
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ export LDFLAGS
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./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'
+ for i in $(find $(dirname ./configure) -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'
+ '[' 1 = 1 ']'
+ '[' x '!=' x-specs=/usr/lib/rpm/redhat/redhat-hardened-ld ']'
++ find . -name ltmain.sh
+ for i in $(find . -name ltmain.sh)
+ /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./ltmain.sh
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-guile --with-python --with-pygtk --disable-static 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing' --with-enhanced-ligand-tools 'RDKIT_LIBS=-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7' 'RDKIT_CXXFLAGS=-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT'
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /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 x86_64-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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for library containing strerror... none required
checking for x86_64-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 whether gcc understands -c and -o together... (cached) yes
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 x86_64-redhat-linux-gnu-g++... no
checking for x86_64-redhat-linux-gnu-c++... no
checking for x86_64-redhat-linux-gnu-gpp... no
checking for x86_64-redhat-linux-gnu-aCC... no
checking for x86_64-redhat-linux-gnu-CC... no
checking for x86_64-redhat-linux-gnu-cxx... no
checking for x86_64-redhat-linux-gnu-cc++... no
checking for x86_64-redhat-linux-gnu-cl.exe... no
checking for x86_64-redhat-linux-gnu-FCC... no
checking for x86_64-redhat-linux-gnu-KCC... no
checking for x86_64-redhat-linux-gnu-RCC... no
checking for x86_64-redhat-linux-gnu-xlC_r... no
checking for x86_64-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... x86_64-redhat-linux-gnu
checking host system type... x86_64-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... 1572864
checking how to convert x86_64-redhat-linux-gnu file names to x86_64-redhat-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-redhat-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-redhat-linux-gnu-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-redhat-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-redhat-linux-gnu-ar... no
checking for ar... ar
checking for archiver @FILE support... @
checking for x86_64-redhat-linux-gnu-strip... no
checking for strip... strip
checking for x86_64-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for x86_64-redhat-linux-gnu-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for 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 -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking what warning flags to pass to the C compiler... -Wall -Wunused
checking what language compliance flags to pass to the C compiler... 
checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused
checking what language compliance flags to pass to the C++ compiler... 
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking for OpenMP flag of C compiler... -fopenmp
checking for x86_64-redhat-linux-gnu-pkg-config... /usr/bin/x86_64-redhat-linux-gnu-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 SQLite3... no
checking for mmdb2... yes
checking for ssm... yes
no
checking for prefixed single-precision FFTW2 (sfftw.h)... 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 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... (cached) /usr/bin/x86_64-redhat-linux-gnu-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 python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages
checking for guile-gtk... 
checking for boostlib >= 1.20.0... yes
checking for python2.7... /usr/bin/python2.7
checking for a version of Python >= '2.1.0'... yes
checking for the distutils Python package... yes
checking for Python include path... -I/usr/include/python2.7
checking for Python library path... -L/usr/lib64 -lpython2.7
checking for Python site-packages path... /usr/lib/python2.7/site-packages
checking python extra libraries... -lpthread -ldl  -lutil -lm
checking python extra linking flags... -Xlinker -export-dynamic
checking consistency of all components of python development environment... yes
checking whether the Boost::Python library is available... yes
checking for exit in -lboost_python... yes
checking libglade... no
checking for Goocanvas... yes
Not using MySQL database
checking for curl >= 7.9.7... ./configure: line 21973: bc: command not found
7.54.1
checking build type... Linux-x86_64-fedora-27-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 pixmaps/Makefile
config.status: creating pixmaps/icons/Makefile
config.status: creating rama-data/Makefile
config.status: creating man/Makefile
config.status: creating pyrogen/Makefile
config.status: creating pyrogen/pyrogen
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
+ 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
+ sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool
+ sed -i 's|$(SHELL) ./config.status;; \\|echo "skipping";; \\|' Makefile
+ cp libtool libtool.tdf
+ make -j2
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing aclocal-1.15 -I macros -I macros
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing autoconf
 cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing automake-1.15 --gnu
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-guile --with-python --with-pygtk --disable-static CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing --with-enhanced-ligand-tools RDKIT_LIBS=-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 RDKIT_CXXFLAGS=-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT build_alias=x86_64-redhat-linux-gnu host_alias=x86_64-redhat-linux-gnu CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /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 x86_64-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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for library containing strerror... none required
checking for x86_64-redhat-linux-gnu-gcc... gcc
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7.54.1
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Making all in auxil
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Making all in compat
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/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.     -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o getopt.lo getopt.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.     -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o getopt1.lo getopt1.c
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c getopt1.c  -fPIC -DPIC -o .libs/getopt1.o
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-compat.la -rpath /usr/lib64 getopt.lo getopt1.lo  
libtool: link: gcc -Wl,--as-needed -shared  -fPIC -DPIC  .libs/getopt.o .libs/getopt1.o   -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8/compat'
Making all in utils
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make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
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make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..    -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-utils.lo coot-utils.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..    -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-fasta.lo coot-fasta.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-utils.cc  -fPIC -DPIC -o .libs/coot-utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-fasta.cc  -fPIC -DPIC -o .libs/coot-fasta.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c dodec.cc  -fPIC -DPIC -o .libs/dodec.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c protein_db_utils.cpp  -fPIC -DPIC -o .libs/protein_db_utils.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c rna_db.cpp  -fPIC -DPIC -o .libs/rna_db.o
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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-0.8.8/protein_db'
Making all in mini-mol
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mini-mol-utils.cc  -fPIC -DPIC -o .libs/mini-mol-utils.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mini-mol.cc  -fPIC -DPIC -o .libs/mini-mol.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c atom-quads.cc  -fPIC -DPIC -o .libs/atom-quads.o
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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" )
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol'
Making all in geometry
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXChargeTable.cpp  -fPIC -DPIC -o .libs/CXXChargeTable.o
In file included from CXXNewHood.h:22:0,
                 from CXXSphereElement.cpp:19:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXCircle.lo CXXCircle.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXSphereTriangle.lo CXXSphereTriangle.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCircle.cpp  -fPIC -DPIC -o .libs/CXXCircle.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereTriangle.cpp  -fPIC -DPIC -o .libs/CXXSphereTriangle.o
In file included from CXXNewHood.h:22:0,
                 from CXXCircle.cpp:12:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXCircleNode.lo CXXCircleNode.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCircleNode.cpp  -fPIC -DPIC -o .libs/CXXCircleNode.o
In file included from CXXNewHood.h:22:0,
                 from CXXCircleNode.cpp:13:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXSphereTriangleEdge.lo CXXSphereTriangleEdge.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereTriangleEdge.cpp  -fPIC -DPIC -o .libs/CXXSphereTriangleEdge.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXCoord.lo CXXCoord.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCoord.cpp  -fPIC -DPIC -o .libs/CXXCoord.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXSurface.lo CXXSurface.cpp
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXCreator.lo CXXCreator.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSurface.cpp  -fPIC -DPIC -o .libs/CXXSurface.o
In file included from CXXNewHood.h:22:0,
                 from CXXSurface.cpp:17:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
CXXSurface.cpp:593:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared(nSelAtoms, SelAtom, cout, unitSphereAtOrigin, vdwBallPntrs, contactMap, ContextSelAtom, splitReentrantProbes) schedule(dynamic, 100) //num_threads(2)
 
CXXSurface.cpp:597:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical(cout)
 
CXXSurface.cpp:618:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (mainTriangles)
 
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCreator.cpp  -fPIC -DPIC -o .libs/CXXCreator.o
CXXSurface.cpp: In member function 'int CXXSurface::calculateVDWFromAtoms(mmdb::PManager, int, int, double, double, bool)':
CXXSurface.cpp:497:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete vdwBallPntrs[i];
                                             ^
CXXSurface.cpp:502:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
    if (contextBallPntrs[i]) delete contextBallPntrs[i];
                                                      ^
CXXSurface.cpp: In member function 'int CXXSurface::calculateAccessibleFromAtoms(mmdb::PManager, int, int, double, double, bool)':
CXXSurface.cpp:549:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete vdwBallPntrs[i];
                                             ^
CXXSurface.cpp:554:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
    if (contextBallPntrs[i]) delete contextBallPntrs[i];
                                                      ^
CXXSurface.cpp: In member function 'int CXXSurface::calculateFromAtoms(mmdb::PManager, int, int, double, double, bool)':
CXXSurface.cpp:634:79: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete static_cast<const CXXAtomBall *>(vdwBallPntrs[i]);
                                                                               ^
CXXSurface.cpp:637:87: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   if (contextBallPntrs[i]) delete static_cast<const CXXAtomBall *>(contextBallPntrs[i]);
                                                                                       ^
CXXSurface.cpp:641:76: warning: deleting object of polymorphic class type 'CXXReentrantProbeBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
        delete static_cast<const CXXReentrantProbeBall *>(reentrantProbes[i]);
                                                                            ^
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXSurfaceVertex.lo CXXSurfaceVertex.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSurfaceVertex.cpp  -fPIC -DPIC -o .libs/CXXSurfaceVertex.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXTorusElement.cpp  -fPIC -DPIC -o .libs/CXXTorusElement.o
In file included from CXXNewHood.h:22:0,
                 from CXXTorusElement.cpp:17:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXTorusNode.cpp  -fPIC -DPIC -o .libs/CXXTorusNode.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXFortranFile.cpp  -fPIC -DPIC -o .libs/CXXFortranFile.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXNewHood.cpp  -fPIC -DPIC -o .libs/CXXNewHood.o
In file included from CXXNewHood.h:22:0,
                 from CXXNewHood.cpp:15:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
CXXNewHood.cpp:345:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (circleNodes)
 
CXXNewHood.cpp:376:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (mainTriangles)
 
CXXNewHood.cpp:409:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (mainTriangles)
 
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXNode.lo CXXNode.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXNode.cpp  -fPIC -DPIC -o .libs/CXXNode.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXQADSurface.lo CXXQADSurface.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXQADSurface.cpp  -fPIC -DPIC -o .libs/CXXQADSurface.o
In file included from CXXNewHood.h:22:0,
                 from CXXQADSurface.h:11,
                 from CXXQADSurface.cpp:1:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXBall.lo CXXBall.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXBall.cpp  -fPIC -DPIC -o .libs/CXXBall.o
In file included from CXXBall.cpp:10:0:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
CXXBall.cpp:34:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared(delta, nBalls, contactMap, aSurface, raggedEdges, insideOrOutside, ballPntrs) schedule(dynamic, 10) //num_threads(2)
 
CXXBall.cpp:83:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared(trimmedBalls, contactMap, insideOrOutside, reformattedEdges, delta, aSurface) schedule(dynamic, 10) //num_threads(2)
 
CXXBall.cpp:197:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared (binnedballs, ballRadiusX2, limits, binWidth, nBins, balls, contactMap) schedule(dynamic,10) //num_threads(2)
 
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXQADSurfaceStaticData.cpp  -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o
In file included from CXXNewHood.h:22:0,
                 from CXXQADSurface.h:11,
                 from CXXQADSurfaceStaticData.cpp:1:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin)
 
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXSpace.lo CXXSpace.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSpace.cpp  -fPIC -DPIC -o .libs/CXXSpace.o
CXXSpace.cpp: In member function 'int CXXSpace::dumpSpaceSlice(int, int, int)':
CXXSpace.cpp:516:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
        if (j == (dim[1]-1))
        ^~
CXXSpace.cpp:518:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         break;
         ^~~~~
CXXSpace.cpp:523:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
        if (j == (dim[1]-1))
        ^~
CXXSpace.cpp:526:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         break;
         ^~~~~
CXXSpace.cpp:563:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
        if (i == (dim[0]-1))
        ^~
CXXSpace.cpp:566:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         break;
         ^~~~~
CXXSpace.cpp:571:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
        if (i == (dim[0]-1))
        ^~
CXXSpace.cpp:575:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         break;
         ^~~~~
CXXSpace.cpp:605:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
        if (i == (dim[0]-1))
        ^~
CXXSpace.cpp:608:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         break;
         ^~~~~
CXXSpace.cpp:613:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
        if (i == (dim[0]-1))
        ^~
CXXSpace.cpp:616:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         break;
         ^~~~~
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I../coot-utils       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o CXXUtils.lo CXXUtils.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXUtils.cpp  -fPIC -DPIC -o .libs/CXXUtils.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-electrostatics.la -rpath /usr/lib64 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 -lmmdb2  -lsrfftw -lsfftw -lmmdb2   
libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/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 -lpthread -lccp4c -lsrfftw -lsfftw -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-electrostatics.so.0 -o .libs/libcoot-electrostatics.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-electrostatics.so.0" && ln -s "libcoot-electrostatics.so.0.0.0" "libcoot-electrostatics.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-electrostatics.so" && ln -s "libcoot-electrostatics.so.0.0.0" "libcoot-electrostatics.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-electrostatics.la" && ln -s "../libcoot-electrostatics.la" "libcoot-electrostatics.la" )
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface'
Making all in coot-surface
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c rgbreps.cc  -fPIC -DPIC -o .libs/rgbreps.o
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libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" )
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -g -O1 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c AngleInfo-theta_2-autogen.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c ppmutil.cc  -fPIC -DPIC -o .libs/ppmutil.o
ppmutil.cc: In member function 'void image_info::readpng(const char*)':
ppmutil.cc:2508:79: 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:2512:9: warning: 'num_trans' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if(row_pointers[i][j]<num_trans){
         ^~
ppmutil.cc:2513:86: 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libccp4mg-utils.la -rpath /usr/lib64 geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo -lpng 
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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" )
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Making all in density-contour
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c Vectors.cpp  -fPIC -DPIC -o .libs/Vectors.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CIsoSurface.cpp  -fPIC -DPIC -o .libs/CIsoSurface.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..     -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o density-contour-triangles.lo density-contour-triangles.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c density-contour-triangles.cc  -fPIC -DPIC -o .libs/density-contour-triangles.o
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libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so")
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Making all in db-main
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c db-strands.cc  -fPIC -DPIC -o .libs/db-strands.o
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libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so")
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mogul.cc  -fPIC -DPIC -o .libs/mogul.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c bfkurt.cc  -fPIC -DPIC -o .libs/bfkurt.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..     -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o kolmogorov.lo kolmogorov.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c kolmogorov.cc  -fPIC -DPIC -o .libs/kolmogorov.o
In file included from mogul.cc:31:0:
mogul-interface.hh: In member function 'coot::mogul_item coot::mogul::parse_angle_line(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&) const':
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_item {
          ^~~~~~~~~~
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_distribution {
          ^~~~~~~~~~~~~~~~~~
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh: In member function 'coot::mogul_item coot::mogul::parse_item_line(const std::vector<std::__cxx11::basic_string<char> >&, int) const':
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::idx_3' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_item {
          ^~~~~~~~~~
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_distribution {
          ^~~~~~~~~~~~~~~~~~
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_item {
          ^~~~~~~~~~
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_distribution {
          ^~~~~~~~~~~~~~~~~~
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::mean' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_item {
          ^~~~~~~~~~
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::median' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::std_dev' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:27:10: warning: '<anonymous>.coot::mogul_item::z' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class mogul_distribution {
          ^~~~~~~~~~~~~~~~~~
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized]
mogul-interface.hh:16:10: warning: '*((void*)(&<anonymous>)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized]
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c stats.cc  -fPIC -DPIC -o .libs/stats.o
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g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..     -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o bfactan.o bfactan.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c cablam.cc  -fPIC -DPIC -o .libs/cablam.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-analysis.la -rpath /usr/lib64 bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2  -lgsl -lgslcblas -lm 
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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" )
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libtool: link: g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-bfactan bfactan.o  ./.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so -lgsl -lgslcblas ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/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 -lmmdb2
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make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal'
Making all in ligand
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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trace.cc:353:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for shared(scores)
 
trace.cc:1202:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for // currently we write out the fragments, not store them
 
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c high-res.cc  -fPIC -DPIC -o .libs/high-res.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-atom-graph.cc  -fPIC -DPIC -o .libs/coot-atom-graph.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c residue-distortions.cc  -fPIC -DPIC -o .libs/residue-distortions.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c sequence-assignment.cc  -fPIC -DPIC -o .libs/sequence-assignment.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-high-res.la -rpath /usr/lib64 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 -lmmdb2  -lmmdb2  
libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o   -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/ideal/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/db-main/.libs -L/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/analysis/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so -lpng /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lgsl -lgslcblas /builddir/build/BUILD/coot-0.8.8/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 -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -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" )
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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" )
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libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/tw.o   -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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" )
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libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c annotation.c  -fPIC -DPIC -o .libs/annotation.o
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c polar_util.c  -fPIC -DPIC -o .libs/polar_util.o
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include  -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o trace.lo trace.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include  -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o axis.lo axis.c
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c trace.c  -fPIC -DPIC -o .libs/trace.o
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c axis.c  -fPIC -DPIC -o .libs/axis.o
trace.c: In function 'gtk_graph_trace_set_data':
trace.c:147:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if (xd[i] > xmax_store)
     ^~
trace.c:149:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  if (xd[i] < xmin_store )
  ^~
trace.c: In function 'gtk_graph_trace_format_marker':
trace.c:259:12: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
            else
            ^~~~
trace.c:261:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
         break;
         ^~~~~
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include  -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o gtkgraph.lo gtkgraph.c
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include  -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o polar.lo polar.c
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c gtkgraph.c  -fPIC -DPIC -o .libs/gtkgraph.o
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c polar.c  -fPIC -DPIC -o .libs/polar.o
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include  -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o smith.lo smith.c
libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c smith.c  -fPIC -DPIC -o .libs/smith.o
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-gtkgraph.la -rpath /usr/lib64 annotation.lo polar_util.lo trace.lo axis.lo gtkgraph.lo polar.lo smith.lo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype  -lm 
libtool: link: gcc -Wl,--as-needed -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 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lm -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8/libgtkgraph'
Making all in lbg
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread      -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK    -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o lbg.lo lbg.cc
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c pi-stacking.cc  -fPIC -DPIC -o .libs/pi-stacking.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c lbg-drag-and-drop.cc  -fPIC -DPIC -o .libs/lbg-drag-and-drop.o
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libtool: link: ( cd ".libs" && rm -f "libcoot-lidia.la" && ln -s "../libcoot-lidia.la" "libcoot-lidia.la" )
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libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/lidia lidia-main.o lbg-callbacks-outer.o -Wl,-export-dynamic  ./.libs/libcoot-lidia.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.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-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/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 -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lm -lutil
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Making all in cootaneer
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c buccaneer-lib.cpp  -fPIC -DPIC -o .libs/buccaneer-lib.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c buccaneer-prot.cpp  -fPIC -DPIC -o .libs/buccaneer-prot.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o buccaneer-sequence.lo buccaneer-sequence.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c buccaneer-sequence.cpp  -fPIC -DPIC -o .libs/buccaneer-sequence.o
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.       -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o cootaneer-sequence.lo cootaneer-sequence.cpp
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c cootaneer-sequence.cpp  -fPIC -DPIC -o .libs/cootaneer-sequence.o
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcootaneer.la -rpath /usr/lib64 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 -lmmdb2  
libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/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 -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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" )
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Making all in cootilus
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nautilus-tools.cpp  -fPIC -DPIC -o .libs/nautilus-tools.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nucleicacid_db.cpp  -fPIC -DPIC -o .libs/nucleicacid_db.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nautilus-ss-find.cpp  -fPIC -DPIC -o .libs/nautilus-ss-find.o
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nautilus-join.cpp  -fPIC -DPIC -o .libs/nautilus-join.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nautilus-target.cpp  -fPIC -DPIC -o .libs/nautilus-target.o
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libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c cootilus-build.cpp  -fPIC -DPIC -o .libs/cootilus-build.o
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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" )
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Making all in goograph
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libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/goograph.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/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 -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 ../utils/.libs/libcoot-utils.so -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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" )
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Making all in pyrogen
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make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.   -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I..  -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o restraints.lo restraints.cc
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/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.   -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I..  -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o restraints-boost.lo restraints-boost.cc
libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c restraints-boost.cc  -fPIC -DPIC -o .libs/restraints-boost.o
cd .. && /bin/sh ./config.status pyrogen/pyrogen
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot_py_restraints.la -rpath /usr/lib64 mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil 
config.status: creating pyrogen/pyrogen
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libtool: link: (cd ".libs" && rm -f "libcoot_py_restraints.so" && ln -s "libcoot_py_restraints.so.0.0.0" "libcoot_py_restraints.so")
libtool: link: ( cd ".libs" && rm -f "libcoot_py_restraints.la" && ln -s "../libcoot_py_restraints.la" "libcoot_py_restraints.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -module  -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o _pyrogen_swig.la -rpath /usr/lib64/python2.7/site-packages pyrogen-swig.lo restraints.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../analysis/libcoot-analysis.la ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2  -lmmdb2  -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil 
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"'  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -module  -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pyrogen_boost.la -rpath /usr/lib64/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python 
libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/restraints-boost.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ./.libs/libcoot_py_restraints.so -ldl -lutil ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/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 -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0
libtool: link: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/pyrogen-swig.o .libs/restraints.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ./.libs/libcoot_py_restraints.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so -lgsl -lgslcblas ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic   -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0
libtool: link: (cd ".libs" && rm -f "pyrogen_boost.so.0" && ln -s "pyrogen_boost.so.0.0.0" "pyrogen_boost.so.0")
libtool: link: (cd ".libs" && rm -f "pyrogen_boost.so" && ln -s "pyrogen_boost.so.0.0.0" "pyrogen_boost.so")
libtool: link: ( cd ".libs" && rm -f "pyrogen_boost.la" && ln -s "../pyrogen_boost.la" "pyrogen_boost.la" )
libtool: link: (cd ".libs" && rm -f "_pyrogen_swig.so.0" && ln -s "_pyrogen_swig.so.0.0.0" "_pyrogen_swig.so.0")
libtool: link: (cd ".libs" && rm -f "_pyrogen_swig.so" && ln -s "_pyrogen_swig.so.0.0.0" "_pyrogen_swig.so")
libtool: link: ( cd ".libs" && rm -f "_pyrogen_swig.la" && ln -s "../_pyrogen_swig.la" "_pyrogen_swig.la" )
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
Making all in src
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src'
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 /bin/sh ./config.status
skipping
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g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o fix-nomenclature.o fix-nomenclature.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-nomenclature.o coot-nomenclature.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o main.o main.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o boot-python.o boot-python.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o atom-overlaps.o atom-overlaps.cc
main.cc: In function 'int main(int, char**)':
main.cc:208:19: warning: 'void g_type_init()' is deprecated [-Wdeprecated-declarations]
       g_type_init(); // for lbg command-line mode, so that
                   ^
In file included from /usr/include/glib-2.0/gobject/gobject.h:24:0,
                 from /usr/include/glib-2.0/gobject/gbinding.h:29,
                 from /usr/include/glib-2.0/glib-object.h:23,
                 from /usr/include/glib-2.0/gio/gioenums.h:28,
                 from /usr/include/glib-2.0/gio/giotypes.h:28,
                 from /usr/include/glib-2.0/gio/gio.h:26,
                 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 main.cc:49:
/usr/include/glib-2.0/gobject/gtype.h:686:23: note: declared here
 void                  g_type_init                    (void);
                       ^~~~~~~~~~~
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o git-revision-count.o git-revision-count.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o scm-boot-guile.o scm-boot-guile.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-analysis.o c-interface-analysis.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-build.o c-interface-build.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-build-morph.o c-interface-build-morph.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-build-main-chain.o c-interface-build-main-chain.cc
In file included from molecule-class-info.h:115:0,
                 from graphics-info.h:75,
                 from c-interface-build.cc:70:
atom-attribute.hh: In function 'int set_atom_attributes(SCM)':
atom-attribute.hh:25:10: warning: '<anonymous>.coot::atom_attribute_setting_help_t::i' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class atom_attribute_setting_help_t {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
atom-attribute.hh: In function 'int set_atom_attributes_py(PyObject*)':
atom-attribute.hh:25:10: warning: '<anonymous>.coot::atom_attribute_setting_help_t::i' may be used uninitialized in this function [-Wmaybe-uninitialized]
    class atom_attribute_setting_help_t {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-build-side-chain.o c-interface-build-side-chain.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-build-symmetry.o c-interface-build-symmetry.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-build-gui.o c-interface-build-gui.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-database.o c-interface-database.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-gui.o c-interface-gui.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-gtk2.o c-interface-gtk2.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-info.o c-interface-info.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-kk.o c-interface-kk.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-ligands.o c-interface-ligands.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-ligands-gui.o c-interface-ligands-gui.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-maps.o c-interface-maps.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-mmdb.o c-interface-mmdb.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-mogul.o c-interface-mogul.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-mogul-scripting.o c-interface-mogul-scripting.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-mutate.o c-interface-mutate.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-ncs.o c-interface-ncs.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-network.o c-interface-network.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-nucleotides.o c-interface-nucleotides.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-python.o c-interface-python.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-pisa.o c-interface-pisa.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-pisa-gui.o c-interface-pisa-gui.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-preferences.o c-interface-preferences.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-refine.o c-interface-refine.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-residues.o c-interface-residues.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-refmac.o c-interface-refmac.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-scm.o c-interface-scm.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-sequence.o c-interface-sequence.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-sfs.o c-interface-sfs.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-sharpen.o c-interface-sharpen.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-superpose.o c-interface-superpose.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-validate.o c-interface-validate.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-view.o c-interface-view.cc
c-interface-validate.cc: In function 'int probe_available_p()':
c-interface-validate.cc:943:30: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
   if (scm_is_true(scm_thunk) == 1) {
                              ^~
In file included from /usr/include/libguile.h:34:0,
                 from graphics-info.h:116,
                 from c-interface-validate.cc:54:
c-interface-validate.cc:943:7: note: add parentheses around left hand side expression to silence this warning
   if (scm_is_true(scm_thunk) == 1) {
       ^
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-widgets.o c-interface-widgets.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-waters.o c-interface-waters.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-waters-gui.o c-interface-waters-gui.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface.o c-interface.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o c-interface-test.o c-interface-test.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o cc-interface-user-defined-atom-colours.o cc-interface-user-defined-atom-colours.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o callbacks.o callbacks.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o cfc.o cfc.cc
In file included from /usr/include/python2.7/pyconfig.h:6:0,
                 from /usr/include/python2.7/Python.h:8,
                 from cfc.hh:28,
                 from cfc.cc:43:
/usr/include/python2.7/pyconfig-64.h:1199:0: warning: "_POSIX_C_SOURCE" redefined
 #define _POSIX_C_SOURCE 200112L
 
In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0,
                 from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494,
                 from /usr/include/c++/7/cstddef:49,
                 from cfc.cc:27:
/usr/include/features.h:260:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 
In file included from /usr/include/python2.7/pyconfig.h:6:0,
                 from /usr/include/python2.7/Python.h:8,
                 from cfc.hh:28,
                 from cfc.cc:43:
/usr/include/python2.7/pyconfig-64.h:1221:0: warning: "_XOPEN_SOURCE" redefined
 #define _XOPEN_SOURCE 600
 
In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0,
                 from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494,
                 from /usr/include/c++/7/cstddef:49,
                 from cfc.cc:27:
/usr/include/features.h:201:0: note: this is the location of the previous definition
 # define _XOPEN_SOURCE 700
 
callbacks.c: In function 'on_phs_cell_choice_ok_button_clicked':
callbacks.c:1790:26: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
   snprintf(tmp_name, 3, "%-d", i);
                          ^~~
callbacks.c:1790:25: note: directive argument in the range [0, 2147483647]
   snprintf(tmp_name, 3, "%-d", i);
                         ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from callbacks.c:26:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o change-dir.o change-dir.cc
change-dir.cc: In function 'void change_directory_maybe()':
change-dir.cc:58:14: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
         chdir(s);
         ~~~~~^~~
change-dir.cc:63:10: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
     chdir(s);
     ~~~~~^~~
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o cmtz-interface.o cmtz-interface.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o command-line.o command-line.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o command-line-extern.o command-line-extern.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-colour.o coot-colour.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-align.o coot-align.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o coot-glue-gtk2.o coot-glue-gtk2.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-hydrogens.o coot-hydrogens.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot_pythonmodule.o coot_pythonmodule.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot-setup-python.o coot-setup-python.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot_wrap_guile.o coot_wrap_guile.cc
In file included from /usr/include/python2.7/pyconfig.h:6:0,
                 from /usr/include/python2.7/Python.h:8,
                 from coot_wrap_guile.cc:4:
/usr/include/python2.7/pyconfig-64.h:1199:0: warning: "_POSIX_C_SOURCE" redefined
 #define _POSIX_C_SOURCE 200112L
 
In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0,
                 from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494,
                 from /usr/include/c++/7/cstddef:49,
                 from coot_wrap_guile.cc:2:
/usr/include/features.h:260:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 
In file included from /usr/include/python2.7/pyconfig.h:6:0,
                 from /usr/include/python2.7/Python.h:8,
                 from coot_wrap_guile.cc:4:
/usr/include/python2.7/pyconfig-64.h:1221:0: warning: "_XOPEN_SOURCE" redefined
 #define _XOPEN_SOURCE 600
 
In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0,
                 from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494,
                 from /usr/include/c++/7/cstddef:49,
                 from coot_wrap_guile.cc:2:
/usr/include/features.h:201:0: note: this is the location of the previous definition
 # define _XOPEN_SOURCE 700
 
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o drag-and-drop.o drag-and-drop.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o draw-generic-display-objects.o draw-generic-display-objects.cc
coot_wrap_guile.cc: In function 'scm_unused_struct* _wrap_IntVector_popN___(SCM)':
coot_wrap_guile.cc:2680:33: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
     gswig_result = scm_from_long(result);
                                 ^
coot_wrap_guile.cc: In function 'scm_unused_struct* _wrap_IntVector_ref(SCM, SCM)':
coot_wrap_guile.cc:2718:33: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
     gswig_result = scm_from_long(result);
                                 ^
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o flev.o flev.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o generic-objects.o generic-objects.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o geometry-graphs.o geometry-graphs.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o get-residue.o get-residue.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o get-monomer.o get-monomer.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o globjects.o globjects.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o globularize.o globularize.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info.o graphics-info.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-defines.o graphics-info-defines.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-graphs.o graphics-info-graphs.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-gui.o graphics-info-gui.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-modelling.o graphics-info-modelling.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-navigation.o graphics-info-navigation.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk1.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-navigation-gtk2.o graphics-info-navigation-gtk2.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-preferences.o graphics-info-preferences.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-network.o graphics-info-network.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-mutate.o graphics-info-mutate.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-lsq.o graphics-info-lsq.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-pick.o graphics-info-pick.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-refmac.o graphics-info-refmac.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-render.o graphics-info-render.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-residues.o graphics-info-residues.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-scripting.o graphics-info-scripting.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-state.o graphics-info-state.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-info-superpose.o graphics-info-superpose.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o graphics-ligand-view.o graphics-ligand-view.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o gl-matrix.o gl-matrix.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o gtk-manual.o gtk-manual.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o gtk-widget-conversion-utils.o gtk-widget-conversion-utils.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o gtk2-interface.o gtk2-interface.c
gtk2-interface.c: In function 'create_coot_references_dialog':
gtk2-interface.c:30439:15: 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:31783:7: warning: 'gdk_pixbuf_unref' is deprecated: Use 'g_object_unref' instead [-Wdeprecated-declarations]
       gdk_pixbuf_unref (multi_residue_torsion_dialog_icon_pixbuf);
       ^~~~~~~~~~~~~~~~
In file included from /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h:34:0,
                 from /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37,
                 from /usr/include/gtk-2.0/gdk/gdkcairo.h:28,
                 from /usr/include/gtk-2.0/gdk/gdk.h:33,
                 from /usr/include/gtk-2.0/gtk/gtk.h:32,
                 from gtk2-interface.c:18:
/usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf-core.h:232:12: note: declared here
 void       gdk_pixbuf_unref    (GdkPixbuf *pixbuf);
            ^~~~~~~~~~~~~~~~
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o interface.o interface.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o lbg-interface.o lbg-interface.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info.o molecule-class-info.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-bonds.o molecule-class-info-bonds.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-maps.o molecule-class-info-maps.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-maps-2.o molecule-class-info-maps-2.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-kdc.o molecule-class-info-kdc.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-dots.o molecule-class-info-dots.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-dots-internal.o molecule-class-info-dots-internal.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-other.o molecule-class-info-other.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-build.o molecule-class-info-build.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-mutate.o molecule-class-info-mutate.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-residues.o molecule-class-info-residues.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-refine.o molecule-class-info-refine.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-kk.o molecule-class-info-kk.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-surface.o molecule-class-info-surface.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-patterson.o molecule-class-info-patterson.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-ncs.o molecule-class-info-ncs.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o molecule-class-info-widget-work.o molecule-class-info-widget-work.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o nsv.o nsv.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o pick.o pick.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o probe-clash-score.o probe-clash-score.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o protein_db-interface.o protein_db-interface.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o read-phs.o read-phs.c
read-phs.c: In function 'phs_pdb_cell_symm':
read-phs.c:239:8: warning: variable 'imol' set but not used [-Wunused-but-set-variable]
    int imol;
        ^~~~
read-phs.c: In function 'do_phs_cell_choice_window':
read-phs.c:146:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:146:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read-phs.c:154:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:154:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read-phs.c:162:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:162:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read-phs.c:170:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:170:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read-phs.c:178:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:178:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read-phs.c:186:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:186:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read-phs.c:194:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=]
       snprintf(tmp_name, 3, "%-d", i);
                              ^~~
read-phs.c:194:29: note: directive argument in the range [0, 2147483647]
       snprintf(tmp_name, 3, "%-d", i);
                             ^~~~~
In file included from /usr/include/stdio.h:862:0,
                 from read-phs.c:27:
/usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __bos (__s), __fmt, __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o read-cif.o read-cif.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o rama_mousey.o rama_mousey.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o rama_plot.o rama_plot.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o restraints-editor.o restraints-editor.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o sdf-interface.o sdf-interface.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o support.o support.c
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o support-gtk2-extras.o support-gtk2-extras.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o testing.o testing.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o testing-2.o testing-2.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o trackball.o trackball.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o sequence-view.o sequence-view.cc
gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused  -c -o seq-view-interface.o seq-view-interface.c
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o user-mods.o user-mods.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o xmap-utils.o xmap-utils.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o view.o view.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o coot_wrap_python.o coot_wrap_python.cc
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE   -pthread  -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread  -DCOOT_USE_GTK2_INTERFACE  -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread  -DHAVE_SSMLIB   -I/usr/include  -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread                       -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused  -c -o density-score-by-residue-src.o density-score-by-residue-src.cc
cd .. && /bin/sh ./config.status src/coot
config.status: creating src/coot
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-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 -lmmdb2  -lmmdb2 		 
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o  ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../db-main/.libs/libcoot-db-main.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/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 ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/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 -lm -lpthread -lccp4c -lmmdb2 -pthread
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-density-score-by-residue-bin 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  -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2  -lmmdb2  -lgsl -lgslcblas -lm 
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-density-score-by-residue-bin density-score-by-residue-src.o  ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/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 ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm -pthread
/bin/sh ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -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  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused   -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-bin main.o boot-python.o atom-overlaps.o git-revision-count.o scm-boot-guile.o c-interface-analysis.o c-interface-build.o c-interface-build-morph.o c-interface-build-main-chain.o c-interface-build-side-chain.o c-interface-build-symmetry.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-mogul-scripting.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-refmac.o c-interface-scm.o c-interface-sequence.o c-interface-sfs.o c-interface-sharpen.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 cc-interface-user-defined-atom-colours.o callbacks.o cfc.o change-dir.o cmtz-interface.o command-line.o command-line-extern.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot-setup-python.o coot_wrap_guile.o drag-and-drop.o draw-generic-display-objects.o flev.o generic-objects.o geometry-graphs.o get-residue.o get-monomer.o globjects.o globularize.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-bonds.o molecule-class-info-maps.o molecule-class-info-maps-2.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-dots-internal.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-patterson.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o probe-clash-score.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 testing-2.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o view.o coot_wrap_python.o  ../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/libcoot-electrostatics.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  		 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2  -lssm -lmmdb2   -lmmdb2  -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil  -pthread  -lguile    -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lpangox-1.0 -lX11 -Wl,--export-dynamic -lgmodule-2.0 -pthread -lglib-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype  -lglut  -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype   -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype  -lgsl -lgslcblas -lm  -lcurl  -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo   -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype  
libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-bin main.o boot-python.o atom-overlaps.o git-revision-count.o scm-boot-guile.o c-interface-analysis.o c-interface-build.o c-interface-build-morph.o c-interface-build-main-chain.o c-interface-build-side-chain.o c-interface-build-symmetry.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-mogul-scripting.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-refmac.o c-interface-scm.o c-interface-sequence.o c-interface-sfs.o c-interface-sharpen.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 cc-interface-user-defined-atom-colours.o callbacks.o cfc.o change-dir.o cmtz-interface.o command-line.o command-line-extern.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot-setup-python.o coot_wrap_guile.o drag-and-drop.o draw-generic-display-objects.o flev.o generic-objects.o geometry-graphs.o get-residue.o get-monomer.o globjects.o globularize.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-bonds.o molecule-class-info-maps.o molecule-class-info-maps-2.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-dots-internal.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-patterson.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o probe-clash-score.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 testing-2.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o view.o coot_wrap_python.o -Wl,-export-dynamic -pthread -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-0.8.8/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-0.8.8/ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../coot-surface/.libs/libcoot-surface.so /builddir/build/BUILD/coot-0.8.8/surface/.libs/libcoot-electrostatics.so ../surface/.libs/libcoot-electrostatics.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/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-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/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 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lssm -lmmdb2 -lpthread -ldl -lutil -lguile -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 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -pthread
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src'
Making all in data
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make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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Making all in man
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 /bin/sh ./config.status
skipping
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make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man'
Making all in rama-data
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data'
Making all in doc
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make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc'
Making all in rcrane
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane'
Making all in pixmaps
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
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 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
Making all in icons
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons'
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 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
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make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
sed -e 's/#GTK2 //'  ./cootrc.template > cootrc
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
+ pushd src
~/build/BUILD/coot-0.8.8/src ~/build/BUILD/coot-0.8.8
+ doxygen coot-dox.cfg
/builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:59: warning: Compound coot::pisa_interface_bond_info_t is not documented.
/builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:299: warning: Compound coot::file_attribs_info_t is not documented.
/builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:45: warning: Compound coot::alias_path_t is not documented.
/builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:287: warning: Compound coot::str_mtime is not documented.
Notice: Output directory `doxygen' does not exist. I have created it for you.
Searching for include files...
Searching for example files...
Searching for images...
Searching for dot files...
Searching for msc files...
Searching for dia files...
Searching for files to exclude
Searching INPUT for files to process...
Reading and parsing tag files
Parsing files
Preprocessing /builddir/build/BUILD/coot-0.8.8/src/c-interface.h...
Parsing file /builddir/build/BUILD/coot-0.8.8/src/c-interface.h...
Preprocessing /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh...
Parsing file /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh...
Building group list...
Building directory list...
Building namespace list...
Building file list...
Building class list...
Associating documentation with classes...
Computing nesting relations for classes...
Building example list...
Searching for enumerations...
Searching for documented typedefs...
Searching for members imported via using declarations...
Searching for included using directives...
Searching for documented variables...
Building interface member list...
Building member list...
Searching for friends...
Searching for documented defines...
Computing class inheritance relations...
Computing class usage relations...
Flushing cached template relations that have become invalid...
Computing class relations...
Add enum values to enums...
Searching for member function documentation...
Creating members for template instances...
Building page list...
Search for main page...
Computing page relations...
Determining the scope of groups...
Sorting lists...
Freeing entry tree
Determining which enums are documented
Computing member relations...
Building full member lists recursively...
Adding members to member groups.
Computing member references...
Inheriting documentation...
Generating disk names...
Adding source references...
Adding xrefitems...
Sorting member lists...
Computing dependencies between directories...
Generating citations page...
Counting data structures...
Resolving user defined references...
Finding anchors and sections in the documentation...
Transferring function references...
Combining using relations...
Adding members to index pages...
Generating style sheet...
Generating search indices...
Generating example documentation...
Generating file sources...
Generating code for file c-interface.h...
Generating code for file cc-interface.hh...
Generating file documentation...
Generating docs for file c-interface.h...
Generating page documentation...
Generating group documentation...
Generating class documentation...
Generating namespace index...
Generating docs for compound coot::alias_path_t...
Generating docs for compound coot::file_attribs_info_t...
Generating docs for compound coot::pisa_interface_bond_info_t...
Generating docs for compound coot::str_mtime...
Generating graph info page...
Generating directory documentation...
Generating index page...
Generating page index...
Generating module index...
Generating namespace index...
Generating namespace member index...
Generating annotated compound index...
Generating alphabetical compound index...
Generating hierarchical class index...
Generating member index...
Generating file index...
Generating file member index...
Generating example index...
finalizing index lists...
writing tag file...
Generating XML output...
Generating XML output for class coot::alias_path_t
Generating XML output for class coot::file_attribs_info_t
Generating XML output for class coot::pisa_interface_bond_info_t
Generating XML output for class coot::str_mtime
Generating XML output for namespace coot
Generating XML output for file c-interface.h
Generating XML output for file cc-interface.hh
lookup cache used 844/65536 hits=1882 misses=845
finished...
~/build/BUILD/coot-0.8.8
~/build/BUILD/coot-0.8.8/doc ~/build/BUILD/coot-0.8.8
+ popd
+ pushd doc
+ make coot-user-manual.pdf
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
xsltproc ../doc/xml2texi.xsl ../src/doxygen/xml/c-interface_8h.xml > c-interface_8h.texi
xsltproc ../doc/xml2texi.xsl ../src/doxygen/xml/cc-interface_8hh.xml > cc-interface_8hh.texi
guile -s ../scheme/snarf-coot-docs.scm ../scheme
/usr/bin/guile-tools
;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0
;;;       or pass the --no-auto-compile argument to disable.
;;; compiling /usr/bin/guile-tools
;;; compiled /builddir/.cache/guile/ccache/2.0-LE-8-2.0/usr/bin/guild.go
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "ncs.texi.tmp" "../scheme/ncs.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "ncs.texi.tmp" "../scheme/ncs.scm") returns status 0
making "ncs.texi" by greping... "ncs.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "bit.texi.tmp" "../scheme/bit.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "bit.texi.tmp" "../scheme/bit.scm") returns status 0
making "bit.texi" by greping... "bit.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "extra-top-level.texi.tmp" "../scheme/extra-top-level.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "extra-top-level.texi.tmp" "../scheme/extra-top-level.scm") returns status 0
making "extra-top-level.texi" by greping... "extra-top-level.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.save.texi.tmp" "../scheme/get-ebi.save.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.save.texi.tmp" "../scheme/get-ebi.save.scm") returns status 0
making "get-ebi.save.texi" by greping... "get-ebi.save.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "clear-backup.texi.tmp" "../scheme/clear-backup.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "clear-backup.texi.tmp" "../scheme/clear-backup.scm") returns status 0
making "clear-backup.texi" by greping... "clear-backup.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-add-linked-cho.texi.tmp" "../scheme/gui-add-linked-cho.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "gui-add-linked-cho.texi.tmp" "../scheme/gui-add-linked-cho.scm") returns status 0
making "gui-add-linked-cho.texi" by greping... "gui-add-linked-cho.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-gui.texi.tmp" "../scheme/coot-gui.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "coot-gui.texi.tmp" "../scheme/coot-gui.scm") returns status 0
making "coot-gui.texi" by greping... "coot-gui.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-hole.texi.tmp" "../scheme/gui-hole.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "gui-hole.texi.tmp" "../scheme/gui-hole.scm") returns status 0
making "gui-hole.texi" by greping... "gui-hole.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "extensions.texi.tmp" "../scheme/extensions.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "extensions.texi.tmp" "../scheme/extensions.scm") returns status 0
making "extensions.texi" by greping... "extensions.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "shelx-extensions.texi.tmp" "../scheme/shelx-extensions.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "shelx-extensions.texi.tmp" "../scheme/shelx-extensions.scm") returns status 0
making "shelx-extensions.texi" by greping... "shelx-extensions.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "redefine-functions.texi.tmp" "../scheme/redefine-functions.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "redefine-functions.texi.tmp" "../scheme/redefine-functions.scm") returns status 0
making "redefine-functions.texi" by greping... "redefine-functions.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-utils.texi.tmp" "../scheme/coot-utils.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "coot-utils.texi.tmp" "../scheme/coot-utils.scm") returns status 0
making "coot-utils.texi" by greping... "coot-utils.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "raster3d.texi.tmp" "../scheme/raster3d.scm/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "raster3d.texi.tmp" "../scheme/raster3d.scm") returns status 0
making "raster3d.texi" by greping... "raster3d.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "3d-generator-import.texi.tmp" "../scheme/3d-generator-import.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "3d-generator-import.texi.tmp" "../scheme/3d-generator-import.scm") returns status 0
making "3d-generator-import.texi" by greping... "3d-generator-import.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "generic-objects.texi.tmp" "../scheme/generic-objects.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "generic-objects.texi.tmp" "../scheme/generic-objects.scm") returns status 0
making "generic-objects.texi" by greping... "generic-objects.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "refmac.texi.tmp" "../scheme/refmac.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "refmac.texi.tmp" "../scheme/refmac.scm") returns status 0
making "refmac.texi" by greping... "refmac.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "libcheck.texi.tmp" "../scheme/libcheck.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "libcheck.texi.tmp" "../scheme/libcheck.scm") returns status 0
making "libcheck.texi" by greping... "libcheck.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "my-readline.texi.tmp" "../scheme/my-readline.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "my-readline.texi.tmp" "../scheme/my-readline.scm") returns status 0
making "my-readline.texi" by greping... "my-readline.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.texi.tmp" "../scheme/get-ebi.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.texi.tmp" "../scheme/get-ebi.scm") returns status 0
making "get-ebi.texi" by greping... "get-ebi.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "dictionary-generators.texi.tmp" "../scheme/dictionary-generators.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "dictionary-generators.texi.tmp" "../scheme/dictionary-generators.scm") returns status 0
making "dictionary-generators.texi" by greping... "dictionary-generators.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "0-auto-rot.texi.tmp" "../scheme/0-auto-rot.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "0-auto-rot.texi.tmp" "../scheme/0-auto-rot.scm") returns status 0
making "0-auto-rot.texi" by greping... "0-auto-rot.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "local-code.texi.tmp" "../scheme/local-code.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "local-code.texi.tmp" "../scheme/local-code.scm") returns status 0
making "local-code.texi" by greping... "local-code.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "matrices.texi.tmp" "../scheme/matrices.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "matrices.texi.tmp" "../scheme/matrices.scm") returns status 0
making "matrices.texi" by greping... "matrices.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "fitting.texi.tmp" "../scheme/fitting.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "fitting.texi.tmp" "../scheme/fitting.scm") returns status 0
making "fitting.texi" by greping... "fitting.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-crash-catcher.texi.tmp" "../scheme/coot-crash-catcher.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "coot-crash-catcher.texi.tmp" "./usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
./scheme/coot-crash-catcher.scm") returns status 0
making "coot-crash-catcher.texi" by greping... "coot-crash-catcher.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "povray.texi.tmp" "../scheme/povray.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "povray.texi.tmp" "../scheme/povray.scm") returns status 0
making "povray.texi" by greping... "povray.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "file-utils.texi.tmp" "../scheme/file-utils.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "file-utils.texi.tmp" "../scheme/file-utils.scm") returns status 0
making "file-utils.texi" by greping... "file-utils.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "junk.texi.tmp" "../scheme/junk.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "junk.texi.tmp" "../scheme/junk.scm") returns status 0
making "junk.texi" by greping... "junk.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-ligand-sliders.texi.tmp" "../scheme/gui-ligand-sliders.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "gui-ligand-sliders.texi.tmp" "../scheme/gui-ligand-sliders.scm") returns status 0
making "gui-ligand-sliders.texi" by greping... "gui-ligand-sliders.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-lsq.texi.tmp" "../scheme/coot-lsq.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "coot-lsq.texi.tmp" "../scheme/coot-lsq.scm") returns status 0
making "coot-lsq.texi" by greping... "coot-lsq.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "mutate.texi.tmp" "../scheme/mutate.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "mutate.texi.tmp" "../scheme/mutate.scm") returns status 0
making "mutate.texi" by greping... "mutate.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "filter.texi.tmp" "../scheme/filter.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "filter.texi.tmp" "../scheme/filter.scm") returns status 0
making "filter.texi" by greping... "filter.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "enhanced-ligand.texi.tmp" "../scheme/enhanced-ligand.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "enhanced-ligand.texi.tmp" "../scheme/enhanced-ligand.scm") returns status 0
making "enhanced-ligand.texi" by greping... "enhanced-ligand.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-prosmart.texi.tmp" "../scheme/gui-prosmart.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "gui-prosmart.texi.tmp" "../scheme/gui-prosmart.scm") returns status 0
making "gui-prosmart.texi" by greping... "gui-prosmart.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "americanisms.texi.tmp" "../scheme/americanisms.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "americanisms.texi.tmp" "../scheme/americanisms.scm") returns status 0
making "americanisms.texi" by greping... "americanisms.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "tips-gui.texi.tmp" "../scheme/tips-gui.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "tips-gui.texi.tmp" "../scheme/tips-gui.scm") returns status 0
making "tips-gui.texi" by greping... "tips-gui.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "demo-script.texi.tmp" "../scheme/demo-script.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "demo-script.texi.tmp" "../scheme/demo-script.scm") returns status 0
making "demo-script.texi" by greping... "demo-script.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
brute-lsqman.texi.tmp" "../scheme/brute-lsqman.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "brute-lsqman.texi.tmp" "../scheme/brute-lsqman.scm") returns status 0
making "brute-lsqman.texi" by greping... "brute-lsqman.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "group-settings.texi.tmp" "../scheme/group-settings.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "group-settings.texi.tmp" "../scheme/group-settings.scm") returns status 0
making "group-settings.texi" by greping... "group-settings.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "bones-reader.texi.tmp" "../scheme/bones-reader.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "bones-reader.texi.tmp" "../scheme/bones-reader.scm") returns status 0
making "bones-reader.texi" by greping... "bones-reader.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "parse-pisa-xml.texi.tmp" "../scheme/parse-pisa-xml.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "parse-pisa-xml.texi.tmp" "../scheme/parse-pisa-xml.scm") returns status 0
making "parse-pisa-xml.texi" by greping... "parse-pisa-xml.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "template-key-bindings.texi.tmp" "../scheme/template-key-bindings.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "template-key-bindings.texi.tmp" "../scheme/template-key-bindings.scm") returns status 0
making "template-key-bindings.texi" by greping... "template-key-bindings.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "contact-score-isolated-ligand.texi.tmp" "../scheme/contact-score-isolated-ligand.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "contact-score-isolated-ligand.texi.tmp" "../scheme/contact-score-isolated-ligand.scm") returns status 0
making "contact-score-isolated-ligand.texi" by greping... "contact-score-isolated-ligand.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "tips.texi.tmp" "../scheme/tips.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "tips.texi.tmp" "../scheme/tips.scm") returns status 0
making "tips.texi" by greping... "tips.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "background-demo.texi.tmp" "../scheme/background-demo.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "background-demo.texi.tmp" "../scheme/background-demo.scm") returns status 0
making "background-demo.texi" by greping... "background-demo.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "trivial.texi.tmp" "../scheme/trivial.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "trivial.texi.tmp" "../scheme/trivial.scm") returns status 0
making "trivial.texi" by greping... "trivial.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot.texi.tmp" "../scheme/coot.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "coot.texi.tmp" "../scheme/coot.scm") returns status 0
making "coot.texi" by greping... "coot.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "user-define-restraints.texi.tmp" "../scheme/user-define-restraints.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "user-define-restraints.texi.tmp" "../scheme/user-define-restraints.scm") returns status 0
making "user-define-restraints.texi" by greping... "user-define-restraints.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "fascinating-things.texi.tmp" "../scheme/fascinating-things.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "fascinating-things.texi.tmp" "../scheme/fascinating-things.scm") returns status 0
making "fascinating-things.te/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
xi" by greping... "fascinating-things.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "run-mogul.texi.tmp" "../scheme/run-mogul.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "run-mogul.texi.tmp" "../scheme/run-mogul.scm") returns status 0
making "run-mogul.texi" by greping... "run-mogul.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "remote-control.texi.tmp" "../scheme/remote-control.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "remote-control.texi.tmp" "../scheme/remote-control.scm") returns status 0
making "remote-control.texi" by greping... "remote-control.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "json-reader.texi.tmp" "../scheme/json-reader.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "json-reader.texi.tmp" "../scheme/json-reader.scm") returns status 0
making "json-reader.texi" by greping... "json-reader.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "ligand-check.texi.tmp" "../scheme/ligand-check.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "ligand-check.texi.tmp" "../scheme/ligand-check.scm") returns status 0
making "ligand-check.texi" by greping... "ligand-check.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "simple.texi.tmp" "../scheme/simple.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "simple.texi.tmp" "../scheme/simple.scm") returns status 0
making "simple.texi" by greping... "simple.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gtkin.texi.tmp" "../scheme/gtkin.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "gtkin.texi.tmp" "../scheme/gtkin.scm") returns status 0
making "gtkin.texi" by greping... "gtkin.texi.tmp" 
exit status: 1
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "jligand.texi.tmp" "../scheme/jligand.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "jligand.texi.tmp" "../scheme/jligand.scm") returns status 0
making "jligand.texi" by greping... "jligand.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "check-for-updates.texi.tmp" "../scheme/check-for-updates.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "check-for-updates.texi.tmp" "../scheme/check-for-updates.scm") returns status 0
making "check-for-updates.texi" by greping... "check-for-updates.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "shelx.texi.tmp" "../scheme/shelx.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "shelx.texi.tmp" "../scheme/shelx.scm") returns status 0
making "shelx.texi" by greping... "shelx.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "cns2coot.texi.tmp" "../scheme/cns2coot.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "cns2coot.texi.tmp" "../scheme/cns2coot.scm") returns status 0
making "cns2coot.texi" by greping... "cns2coot.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "jligand-gui.texi.tmp" "../scheme/jligand-gui.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "jligand-gui.texi.tmp" "../scheme/jligand-gui.scm") returns status 0
making "jligand-gui.texi" by greping... "jligand-gui.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "snarf-coot-docs.texi.tmp" "../scheme/snarf-coot-docs.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "snarf-coot-docs.texi.tmp" "../scheme/snarf-coot-docs.scm") returns status 0
making "snarf-coot-docs.texi" by greping... "snarf-coot-docs.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "hello.texi.tmp" "../scheme/hello.scm") > snarf.log
exit /usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/guile-tools
/usr/bin/grep
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
/usr/bin/wc
status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "hello.texi.tmp" "../scheme/hello.scm") returns status 0
making "hello.texi" by greping... "hello.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-recent-pdbe.texi.tmp" "../scheme/get-recent-pdbe.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "get-recent-pdbe.texi.tmp" "../scheme/get-recent-pdbe.scm") returns status 0
making "get-recent-pdbe.texi" by greping... "get-recent-pdbe.texi.tmp" 
exit status: 0
INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gap.texi.tmp" "../scheme/gap.scm") > snarf.log
exit status: 0
guile-tools ("doc-snarf" "--texinfo" "-o" "gap.texi.tmp" "../scheme/gap.scm") returns status 0
making "gap.texi" by greping... "gap.texi.tmp" 
exit status: 1
menu section processing "c-interface_8h.texi"
menu section processing "cc-interface_8hh.texi"
menu section processing "ncs.texi"
menu section processing "extra-top-level.texi"
menu section processing "clear-backup.texi"
menu section processing "gui-add-linked-cho.texi"
menu section processing "coot-gui.texi"
menu section processing "redefine-functions.texi"
menu section processing "coot-utils.texi"
menu section processing "raster3d.texi"
menu section processing "3d-generator-import.texi"
menu section processing "generic-objects.texi"
menu section processing "refmac.texi"
menu section processing "libcheck.texi"
menu section processing "get-ebi.texi"
menu section processing "dictionary-generators.texi"
menu section processing "fitting.texi"
menu section processing "coot-crash-catcher.texi"
menu section processing "povray.texi"
menu section processing "gui-ligand-sliders.texi"
menu section processing "coot-lsq.texi"
menu section processing "mutate.texi"
menu section processing "filter.texi"
menu section processing "americanisms.texi"
menu section processing "tips-gui.texi"
menu section processing "brute-lsqman.texi"
menu section processing "group-settings.texi"
menu section processing "parse-pisa-xml.texi"
menu section processing "contact-score-isolated-ligand.texi"
menu section processing "tips.texi"
menu section processing "background-demo.texi"
menu section processing "coot.texi"
menu section processing "user-define-restraints.texi"
menu section processing "fascinating-things.texi"
menu section processing "run-mogul.texi"
menu section processing "remote-control.texi"
menu section processing "ligand-check.texi"
menu section processing "jligand.texi"
menu section processing "check-for-updates.texi"
menu section processing "shelx.texi"
menu section processing "cns2coot.texi"
menu section processing "jligand-gui.texi"
menu section processing "snarf-coot-docs.texi"
menu section processing "hello.texi"
menu section processing "get-recent-pdbe.texi"
all-useful-texis: ("menu-section.texi" "c-interface_8h-section.texi" "c-interface_8h.texi" "cc-interface_8hh-section.texi" "cc-interface_8hh.texi" "ncs-section.texi" "ncs.texi" "extra-top-level-section.texi" "extra-top-level.texi" "clear-backup-section.texi" "clear-backup.texi" "gui-add-linked-cho-section.texi" "gui-add-linked-cho.texi" "coot-gui-section.texi" "coot-gui.texi" "redefine-functions-section.texi" "redefine-functions.texi" "coot-utils-section.texi" "coot-utils.texi" "raster3d-section.texi" "raster3d.texi" "3d-generator-import-section.texi" "3d-generator-import.texi" "generic-objects-section.texi" "generic-objects.texi" "refmac-section.texi" "refmac.texi" "libcheck-section.texi" "libcheck.texi" "get-ebi-section.texi" "get-ebi.texi" "dictionary-generators-section.texi" "dictionary-generators.texi" "fitting-section.texi" "fitting.texi" "coot-crash-catcher-section.texi" "coot-crash-catcher.texi" "povray-section.texi" "povray.texi" "gui-ligand-sliders-section.texi" "gui-ligand-sliders.texi" "coot-lsq-section.texi" "coot-lsq.texi" "mutate-section.texi" "mutate.texi" "filter-section.texi" "filter.texi" "americanisms-section.texi" "americanisms.texi" "tips-gui-section.texi" "tips-gui.texi" "brute-lsqman-section.texi" "brute-lsqman.texi" "group-settings-section.texi" "group-setti/usr/bin/cat
ngs.texi" "parse-pisa-xml-section.texi" "parse-pisa-xml.texi" "contact-score-isolated-ligand-section.texi" "contact-score-isolated-ligand.texi" "tips-section.texi" "tips.texi" "background-demo-section.texi" "background-demo.texi" "coot-section.texi" "coot.texi" "user-define-restraints-section.texi" "user-define-restraints.texi" "fascinating-things-section.texi" "fascinating-things.texi" "run-mogul-section.texi" "run-mogul.texi" "remote-control-section.texi" "remote-control.texi" "ligand-check-section.texi" "ligand-check.texi" "jligand-section.texi" "jligand.texi" "check-for-updates-section.texi" "check-for-updates.texi" "shelx-section.texi" "shelx.texi" "cns2coot-section.texi" "cns2coot.texi" "jligand-gui-section.texi" "jligand-gui.texi" "snarf-coot-docs-section.texi" "snarf-coot-docs.texi" "hello-section.texi" "hello.texi" "get-recent-pdbe-section.texi" "get-recent-pdbe.texi")
exit status: 0
;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0
;;;       or pass the --no-auto-compile argument to disable.
;;; compiling /builddir/build/BUILD/coot-0.8.8/doc/../scheme/snarf-coot-docs.scm
;;; compiled /builddir/.cache/guile/ccache/2.0-LE-8-2.0/builddir/build/BUILD/coot-0.8.8/scheme/snarf-coot-docs.scm.go
;;; compiling /builddir/build/BUILD/coot-0.8.8/doc/../scheme/filter.scm
;;; compiled /builddir/.cache/guile/ccache/2.0-LE-8-2.0/builddir/build/BUILD/coot-0.8.8/scheme/filter.scm.go
if [ ! -e coot-plain-2.eps ] ; then cp ../doc/coot-plain-2.ps coot-plain-2.eps ; fi
texi2dvi ../doc/coot-user-manual.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex)
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conditionals, indexing, sectioning, toc, environments, defuns, macros,
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[1] [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 
[1] [2] Cross reference values unknown; you must run TeX again. [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
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
[21] [22] [23]
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[]@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph
ere-size
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[]@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select
ion-string-1
[24]
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[]@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i
d imol-ref
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[]@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re
f chain-id-ref
[25]
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[]@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno 
en-dresno
Chapter 5 [26] [27] [28]
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[][][] |
[29] [30]
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[]@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno 
alt-loc
[31] [32] [33]
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@textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this 
fragment[][]@textrm .
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[]@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol
-coords imol-map
[34] [35] [36]
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[]@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f
rom the
[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
[38] [39] [40] [41] [42]
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[]@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c
hain-id
[43] [44] [45] [46] Chapter 6 [47]
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[]@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co
lumn-
[48]
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[]@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space-
group-name a b
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[]@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f
ile-name
[49] [50]
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[]@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin
g[]@textrm ) the map will be
[51] [52] [53]
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[]@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0
.2358
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[]@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn
o-start
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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]
(/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66]
[67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
[82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96]
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[110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121]
[122] [123] [124] [125] [126] [127] [128] [129]
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[178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189])
Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi
[191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13
[201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202]
[203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]
[215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226]
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[263] [264] [265] [266] [267]
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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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[280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291]
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315]
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
[328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 2073) in paragraph at lines 13241--13286
 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i
d size mm-size
[364] [365] [366]
Underfull \hbox (badness 2393) in paragraph at lines 13596--13605
 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation-
stats-scm
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 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand
Underfull \hbox (badness 2951) in paragraph at lines 13625--13627
 []@textrm JLigand sends Coot a file that con-tains file-names for the link and
 new
[367] [368] [369]
Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865
 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te
xttt "@textrm http://www.ebi.ac.uk/pdbe-|
) (Concept Index) [370] (Function Index) [371] [372] )
(see the transcript file for additional information)
Output written on coot-user-manual.dvi (375 pages, 920544 bytes).
Transcript written on coot-user-manual.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex)
 restricted \write18 enabled.
entering extended mode
(./../doc/coot-user-manual.texi
(/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex
Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables,
conditionals, indexing, sectioning, toc, environments, defuns, macros,
cross references, insertions,
(/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.aux)
(coot-plain-2.eps
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[1] [2] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.toc [-1]
[-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15]
[-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27]
[-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39]
[-40] [-41] [-42]) [-43] Chapter 1
Underfull \hbox (badness 2556) in paragraph at lines 368--371
 @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]
Underfull \hbox (badness 10000) in paragraph at lines 1221--1222
[]@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine-
[13] [14]
Underfull \hbox (badness 3039) in paragraph at lines 1393--1398
[]@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]
Underfull \hbox (badness 10000) in paragraph at lines 1813--1814
[]@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i
d m11 m12 m13
[21] [22] [23]
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[]@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph
ere-size
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[]@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select
ion-string-1
[24]
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[]@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i
d imol-ref
Underfull \hbox (badness 10000) in paragraph at lines 2165--2166
[]@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re
f chain-id-ref
[25]
Underfull \hbox (badness 10000) in paragraph at lines 2188--2189
[]@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno 
en-dresno
Chapter 5 [26] [27] [28]
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[][][] |
[29] [30]
Underfull \hbox (badness 10000) in paragraph at lines 2574--2575
[]@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno 
alt-loc
[31] [32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2801--2810
@textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this 
fragment[][]@textrm .
Underfull \hbox (badness 10000) in paragraph at lines 2849--2850
[]@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol
-coords imol-map
[34] [35] [36]
Underfull \hbox (badness 2073) in paragraph at lines 3048--3051
[]@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f
rom the
[37]
Underfull \hbox (badness 3954) in paragraph at lines 3120--3123
[]@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling 
-> Replace
Underfull \hbox (badness 4467) in paragraph at lines 3164--3167
[]@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr
m '[] and a dic-tio-nary file
[38] [39] [40] [41] [42]
Underfull \hbox (badness 10000) in paragraph at lines 3514--3515
[]@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c
hain-id
[43] [44] [45] [46] Chapter 6 [47]
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[]@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co
lumn-
[48]
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[]@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space-
group-name a b
Underfull \hbox (badness 10000) in paragraph at lines 3955--3956
[]@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f
ile-name
[49] [50]
Underfull \hbox (badness 4328) in paragraph at lines 4147--4155
[]@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin
g[]@textrm ) the map will be
[51] [52] [53]
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[]@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0
.2358
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[]@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn
o-start
Underfull \hbox (badness 10000) in paragraph at lines 4353--4354
@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]
Underfull \hbox (badness 2662) in paragraph at lines 4721--4725
[]@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]
(/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66]
[67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
[82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96]
[97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109]
[110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121]
[122] [123] [124] [125] [126] [127] [128] [129]
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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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[142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153]
[154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165]
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189])
Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi
[191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13
[201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202]
[203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]
[215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226]
[227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238]
[239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250]
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[263] [264] [265] [266] [267]
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 in the
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[280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291]
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315]
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
[328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363]
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 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i
d size mm-size
[364] [365] [366]
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 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation-
stats-scm
Underfull \hbox (badness 10000) in paragraph at lines 13596--13605
 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand
Underfull \hbox (badness 2951) in paragraph at lines 13625--13627
 []@textrm JLigand sends Coot a file that con-tains file-names for the link and
 new
[367] [368] [369]
Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865
 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te
xttt "@textrm http://www.ebi.ac.uk/pdbe-|
) (Concept Index) [370]
(/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.cps [371] [372])
(Function Index) [373]
(/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.fns [374] [375] [376]
[377] [378] [379] [380] [381] [382] [383] [384]) [385] )
(see the transcript file for additional information)
Output written on coot-user-manual.dvi (430 pages, 1867792 bytes).
Transcript written on coot-user-manual.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex)
 restricted \write18 enabled.
entering extended mode
(./../doc/coot-user-manual.texi
(/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex
Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables,
conditionals, indexing, sectioning, toc, environments, defuns, macros,
cross references, insertions,
(/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
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[1] [2] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.toc [-1]
[-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15]
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[-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39]
[-40] [-41] [-42]) [-43] 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-
[13] [14]
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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
[21] [22] [23]
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 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i
d size mm-size
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 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation-
stats-scm
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 new
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 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te
xttt "@textrm http://www.ebi.ac.uk/pdbe-|
) (Concept Index) [370]
(/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.cps [371] [372])
(Function Index) [373]
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[377] [378] [379] [380] [381] [382] [383] [384]) [385] )
(see the transcript file for additional information)
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ps2pdf coot-user-manual.ps
+ make coot-keys-and-buttons.pdf
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
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skipping
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(see the transcript file for additional information)
Output written on crib-sheet.dvi (3 pages, 7008 bytes).
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This is dvips(k) 5.996 Copyright 2016 Radical Eye Software (www.radicaleye.com)
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ps2pdf crib-sheet.ps
cp crib-sheet.pdf coot-keys-and-buttons.pdf
+ popd
~/build/BUILD/coot-0.8.8
+ exit 0
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+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64
++ dirname /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64
+ cd coot-0.8.8
+ make install DESTDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 'INSTALL=install -p'
 /bin/sh ./config.status
skipping
Making install in auxil
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Making install in catcheck
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Making install in rama
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Making install in sec-str
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Making install in strand-analysis
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Making install in vectors
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
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skipping
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skipping
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make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil'
Making install in scheme
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/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-0.8.8-2.fc27.x86_64/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 3d-generator-import.scm gui-hole.scm gui-prosmart.scm get-recent-pdbe.scm json-reader.scm jligand.scm jligand-gui.scm redefine-functions.scm user-define-restraints.scm template-key-bindings.scm gui-add-linked-cho.scm ligand-check.scm run-mogul.scm contact-score-isolated-ligand.scm enhanced-ligand.scm gui-ligand-sliders.scm dictionary-generators.scm '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/scheme'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme'
Making install in python
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
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cd .. && /bin/sh ./config.status python/coot_load_modules.py
config.status: creating python/coot_load_modules.py
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
 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 3d_generator_import.py gui_hole.py gui_prosmart.py get_recent_pdbe.py jligand.py jligand_gui.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
 install -p -m 644 redefine_functions.py user_define_restraints.py template_key_bindings.py gui_add_linked_cho.py ligand_check.py run_mogul.py contact_score_isolated_ligand.py gui_contact_score_isolated_ligand.py enhanced_ligand.py gui_ligand_sliders.py dictionary_generators.py coot_toolbuttons.py rcrane_loader.py pdbe_validation_data.py ligand_validation_sliders.py chemical_feature_clusters.py res_spec_utils.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
Byte-compiling python modules...
coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycoot_toolbuttons.pyrcrane_loader.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py
Byte-compiling python modules (optimized versions) ...
coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycoot_toolbuttons.pyrcrane_loader.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python'
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Making install in pdb-templates
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skipping
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 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/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 link-by-torsion-to-pyranose-core-ALPHA1-2.tab link-by-torsion-to-pyranose-core-ALPHA1-3.tab link-by-torsion-to-FUC-core-ALPHA1-3.tab link-by-torsion-to-pyranose-core-ALPHA1-6.tab link-by-torsion-to-pyranose-core-ALPHA2-3.tab link-by-torsion-to-pyranose-core-BETA1-3.tab link-by-torsion-to-pyranose-core-BETA1-4.tab link-by-torsion-to-pyranose-core-NAG-ASN.tab link-by-torsion-to-pyranose-core-XYP-BMA.tab NAG-decorations.tab BMA-decorations.tab MAN-decorations.tab GLC-decorations.tab GAL-decorations.tab FUC-decorations.tab XYP-decorations.tab theor-helix-70.pdb '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
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Making install in macros
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skipping
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Making install in compat
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skipping
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skipping
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 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-compat.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-compat.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/compat'
 install -p -m 644 coot-getopt.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/compat'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/compat'
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Making install in utils
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/utils'
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 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/utils'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-utils.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/utils'
 install -p -m 644 coot-utils.hh coot-fasta.hh dodec.hh win-compat.hh ctpl_stl.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/utils'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils'
Making install in protein_db
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-protein-db.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-protein-db.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/protein_db'
 install -p -m 644 protein_db.h protein_db_utils.h rna_db.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/protein_db'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/protein_db'
 install -p -m 644 protein.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/protein_db'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db'
Making install in mini-mol
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-mini-mol.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-mini-mol.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/mini-mol; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-mini-mol.la -rpath /usr/lib64 mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o   -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0
libtool: install: install -p .libs/libcoot-mini-mol.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/mini-mol'
 install -p -m 644 mini-mol.hh mini-mol-utils.hh atom-quads.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/mini-mol'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol'
Making install in geometry
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-geometry.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-geometry.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/geometry; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-geometry.la -rpath /usr/lib64 protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo chem_mods.lo srs-interface.lo protein-donor-acceptors.lo lbg-graph.lo dreiding.lo dict-utils.lo cif-parse.lo main-chain.lo residue-and-atom-specs.lo mol-utils-2.lo ../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 -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/srs-interface.o .libs/protein-donor-acceptors.o .libs/lbg-graph.o .libs/dreiding.o .libs/dict-utils.o .libs/cif-parse.o .libs/main-chain.o .libs/residue-and-atom-specs.o .libs/mol-utils-2.o   -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
  /bin/sh ../libtool   --mode=install install -p coot-compare-dictionaries coot-make-shelx-restraints coot-available-comp-id '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-compare-dictionaries /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-compare-dictionaries
libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-make-shelx-restraints /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-make-shelx-restraints
libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-available-comp-id /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-available-comp-id
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/geometry'
 install -p -m 644 protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interface.hh dict-utils.hh dict-mismatches.hh energy-lib.hh match-results.hh hb-types.hh main-chain.hh residue-and-atom-specs.hh chem_mods.hh mol-utils-2.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/geometry'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry'
Making install in coot-utils
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /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-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-coord-utils.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coord-utils.la -rpath /usr/lib64 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 glyco-torsions.lo coot-least-squares.lo atom-overlaps.lo reduce.lo ../geometry/libcoot-geometry.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/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 .libs/glyco-torsions.o .libs/coot-least-squares.o .libs/atom-overlaps.o .libs/reduce.o   -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.la
libtool: warning: relinking 'libcoot-shelx.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-shelx.la -rpath /usr/lib64 coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/coot-shelx-ins.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -lcoot-utils -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.la
libtool: warning: relinking 'libcoot-coord-extras.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coord-extras.la -rpath /usr/lib64 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 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/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-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.la
libtool: warning: relinking 'libcoot-map-utils.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-map-utils.la -rpath /usr/lib64 coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo libcoot-coord-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/coot-map-utils.o .libs/peak-search.o .libs/peak-search-from-list.o .libs/trim.o .libs/xmap-stats.o .libs/maps-spherical.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.la
libtool: warning: relinking 'libcoot-map-heavy.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-map-heavy.la -rpath /usr/lib64 coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/coot-map-heavy.o .libs/coot-fffear.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coot-utils'
 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 emma.hh glyco-torsions.hh coot-least-squares.hh coot-density-stats.hh atom-overlaps.hh reduce.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coot-utils'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils'
Making install in surface
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-electrostatics.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-electrostatics.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so.0 || { rm -f libcoot-electrostatics.so.0 && ln -s libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so || { rm -f libcoot-electrostatics.so && ln -s libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so; }; })
libtool: install: install -p .libs/libcoot-electrostatics.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface'
Making install in coot-surface
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-surface.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-surface.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-surface; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-surface.la -rpath /usr/lib64 coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/coot-surface.o .libs/rgbreps.o   -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-electrostatics -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface'
Making install in lidia-core
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-lidia-core.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-lidia-core.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/lidia-core; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-lidia-core.la -rpath /usr/lib64 lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo cod-types.lo bond-record-container-t.lo cod-atom-type-t.lo cod-atom-types.lo bond-table-record-t.lo chemical-feature-clusters.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la ../coot-utils/libcoot-coord-utils.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/lbg-shared.o .libs/lbg-molfile.o .libs/lig-build.o .libs/rdkit-interface.o .libs/cod-types.o .libs/bond-record-container-t.o .libs/cod-atom-type-t.o .libs/cod-atom-types.o .libs/bond-table-record-t.o .libs/chemical-feature-clusters.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lidia-core'
 install -p -m 644 lbg-shared.hh lbg-molfile.hh lig-build.hh rdkit-interface.hh use-rdkit.hh cod-types.hh neighbour-sorter.hh bond-record-container-t.hh bond-table-record-t.hh cod-atom-types.hh cod-atom-type-t.hh primes.hh chemical-feature-clusters.hh third-neighbour-info-t.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lidia-core'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lidia-core'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lidia-core'
Making install in coords
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coords'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coords'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-coords.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-coords.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coords; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coords.la -rpath /usr/lib64 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 phenix-geo.lo phenix-geo-bonds.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 -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/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 .libs/phenix-geo.o .libs/phenix-geo-bonds.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-shelx -lcoot-lidia-core -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 -lgsl -lgslcblas -lcoot-utils -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coords'
 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 phenix-geo.hh ramachandran-container.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coords'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords'
Making install in angles
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-AngleInfo.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-AngleInfo.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/angles'
 install -p -m 644 AngleInfo.h ncube.h wrapped-ncube.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/angles'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles'
Making install in skeleton
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-skeleton.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-skeleton.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/skeleton; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-skeleton.la -rpath /usr/lib64 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 -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-AngleInfo -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/skeleton'
 install -p -m 644 graphical_skel.h dm-utils.h BuildCas.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/skeleton'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton'
Making install in ccp4mg-utils
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libccp4mg-utils.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libccp4mg-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ccp4mg-utils'
 install -p -m 644 geomutil.h mgtree.h cartesian.h matrix.h quat.h ppmutil.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ccp4mg-utils'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils'
Making install in density-contour
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/density-contour'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/density-contour'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-isosurface.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-isosurface.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/density-contour; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-isosurface.la -rpath /usr/lib64 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 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/density-contour'
 install -p -m 644 Vectors.h CIsoSurface.h density-contour-triangles.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/density-contour'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/density-contour'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/density-contour'
Making install in db-main
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/db-main'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/db-main'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-db-main.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-db-main.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/db-main; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-db-main.la -rpath /usr/lib64 db-main.lo db-strands.lo ../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 -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/db-main.o .libs/db-strands.o   -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lgsl -lgslcblas -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 -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/db-main'
 install -p -m 644 db-main.hh db-strands.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/db-main'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/db-main'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/db-main'
Making install in analysis
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/analysis'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/analysis'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-analysis.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-analysis.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/analysis; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-analysis.la -rpath /usr/lib64 bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2 -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
  /bin/sh ../libtool   --mode=install install -p coot-bfactan '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
libtool: warning: 'libcoot-analysis.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-bfactan /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-bfactan
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/analysis'
 install -p -m 644 bfkurt.hh mogul-interface.hh stats.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/analysis'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis'
Making install in ideal
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 install -p coot-mini-rsr '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-ideal.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-ideal.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/ideal; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ideal.la -rpath /usr/lib64 simple-restraint.lo mods.lo distortion.lo chirals.lo flanking.lo gradients.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo coot-compare-residues.lo link-restraints.lo parallel-planes.lo trans-peptide.lo model-bond-deltas.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 -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/simple-restraint.o .libs/mods.o .libs/distortion.o .libs/chirals.o .libs/flanking.o .libs/gradients.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 .libs/coot-compare-residues.o .libs/link-restraints.o .libs/parallel-planes.o .libs/trans-peptide.o .libs/model-bond-deltas.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec'
  /bin/sh ../libtool   --mode=install install -p mini-rsr-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec'
libtool: warning: './libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/mini-rsr-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/mini-rsr-bin
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ideal'
 install -p -m 644 test-indexing.hh simple-restraint.hh pepflip.hh regularize-minimol.hh lograma.h parallel-planes.hh torsion-bonds.hh extra-restraints.hh model-bond-deltas.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ideal'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal'
Making install in ligand
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 install -p findwaters findligand '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-ligand.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-ligand.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/ligand; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ligand.la -rpath /usr/lib64 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 trace.lo trace-2.lo multi-peptide.lo ligands-db.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 ../analysis/libcoot-analysis.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 -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/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 .libs/trace.o .libs/trace-2.o .libs/multi-peptide.o .libs/ligands-db.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec'
  /bin/sh ../libtool   --mode=install install -p findligand-bin findwaters-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec'
libtool: warning: './libcoot-ligand.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64'
libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/findligand-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findligand-bin
libtool: warning: './libcoot-ligand.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64'
libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/findwaters-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findwaters-bin
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data'
 install -p -m 644 ligands-2016.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ligand'
 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 trace.hh multi-peptide.hh ligands-db.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ligand'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand'
Making install in high-res
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-high-res.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-high-res.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/high-res; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-high-res.la -rpath /usr/lib64 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 -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o   -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/ideal/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/db-main/.libs -L/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/analysis/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-ligand -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/high-res'
 install -p -m 644 high-res.hh coot-atom-graph.hh coot-node-info.hh sequence-assignment.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/high-res'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res'
Making install in build
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-cabuild.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-cabuild.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/build; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-cabuild.la -rpath /usr/lib64 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 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/CalphaBuild.o   -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-AngleInfo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/build'
 install -p -m 644 CalphaBuild.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/build'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/build'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/build'
Making install in greg-tests
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/greg-tests'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/greg-tests'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
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-0.8.8/greg-tests'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/greg-tests'
Making install in python-tests
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python-tests'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python-tests'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
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-0.8.8/python-tests'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python-tests'
Making install in tw
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/tw'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/tw'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-tw.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-tw.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/tw'
 install -p -m 644 coot-tw.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/tw'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw'
Making install in libgtkgraph
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-gtkgraph.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcoot-gtkgraph.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph'
Making install in lbg
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-lidia.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-lidia.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/lbg; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-lidia.la -rpath /usr/lib64 lbg.lo lbg-flev.lo wmolecule.lo lbg-search.lo residue-circles.lo pi-stacking.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo qed-properties.lo ../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 -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/lbg.o .libs/lbg-flev.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/pi-stacking.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o .libs/qed-properties.o   -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-lidia-core -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 -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic   -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
  /bin/sh ../libtool   --mode=install install -p lidia '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
libtool: warning: './libcoot-lidia.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/lidia /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/lidia
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/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-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia'
 install -p -m 644 __init__.py fetch.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia'
Byte-compiling python modules...
__init__.pyfetch.py
Byte-compiling python modules (optimized versions) ...
__init__.pyfetch.py
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lbg'
 install -p -m 644 lbg.hh w-atom.hh w-bond.hh wmolecule.hh topological-equivalence.hh flev-annotations.hh graphics-c-interface-functions.hh lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh solvent-exposure-difference.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lbg'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
 install -p -m 644 lbg.glade lbg-callbacks.cc '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg'
Making install in cootaneer
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcootaneer.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcootaneer.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
 install -p -m 644 cootaneer-llk-2.40.dat '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer'
Making install in cootilus
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcootilus.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: install: install -p .libs/libcootilus.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
 install -p -m 644 nautilus_lib.pdb '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus'
Making install in goograph
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot-goograph.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot-goograph.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/goograph; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-goograph.la -rpath /usr/lib64 goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/goograph.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-lidia-core -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 -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-utils -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64 && { 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-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph'
Making install in pyrogen
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 install -p pyrogen '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
 /bin/sh ../libtool   --mode=install install -p   libcoot_py_restraints.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64'
libtool: warning: relinking 'libcoot_py_restraints.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot_py_restraints.la -rpath /usr/lib64 mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/mmff-restraints.o .libs/py-restraints.o   -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -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 -lccp4c -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic   -Wl,-soname -Wl,libcoot_py_restraints.so.0 -o .libs/libcoot_py_restraints.so.0.0.0
libtool: install: install -p .libs/libcoot_py_restraints.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so.0 || { rm -f libcoot_py_restraints.so.0 && ln -s libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so || { rm -f libcoot_py_restraints.so && ln -s libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so; }; })
libtool: install: install -p .libs/libcoot_py_restraints.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.la
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages'
 /bin/sh ../libtool   --mode=install install -p   _pyrogen_swig.la pyrogen_boost.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages'
libtool: warning: relinking '_pyrogen_swig.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o _pyrogen_swig.la -rpath /usr/lib64/python2.7/site-packages pyrogen-swig.lo restraints.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../analysis/libcoot-analysis.la ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/pyrogen-swig.o .libs/restraints.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot_py_restraints -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lcoot-analysis -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic   -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0
libtool: install: install -p .libs/_pyrogen_swig.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f _pyrogen_swig.so.0.0.0 _pyrogen_swig.so.0 || { rm -f _pyrogen_swig.so.0 && ln -s _pyrogen_swig.so.0.0.0 _pyrogen_swig.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f _pyrogen_swig.so.0.0.0 _pyrogen_swig.so || { rm -f _pyrogen_swig.so && ln -s _pyrogen_swig.so.0.0.0 _pyrogen_swig.so; }; })
libtool: install: install -p .libs/_pyrogen_swig.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.la
libtool: warning: relinking 'pyrogen_boost.la'
libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool"  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pyrogen_boost.la -rpath /usr/lib64/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64)
libtool: relink: g++  -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o  .libs/restraints-boost.o   -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot_py_restraints -ldl -lutil -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coord-extras -lcoot-coords -lcoot-shelx -lcoot-lidia-core -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 -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro   -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0
libtool: install: install -p .libs/pyrogen_boost.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.so.0.0.0
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f pyrogen_boost.so.0.0.0 pyrogen_boost.so.0 || { rm -f pyrogen_boost.so.0 && ln -s pyrogen_boost.so.0.0.0 pyrogen_boost.so.0; }; })
libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f pyrogen_boost.so.0.0.0 pyrogen_boost.so || { rm -f pyrogen_boost.so && ln -s pyrogen_boost.so.0.0.0 pyrogen_boost.so; }; })
libtool: install: install -p .libs/pyrogen_boost.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.la
libtool: warning: remember to run 'libtool --finish /usr/lib64/python2.7/site-packages'
make  install-exec-hook
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[3]: Nothing to be done for 'install-exec-hook'.
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
 install -p -m 644 pyrogen.py atom_types.py jay_util.py tautomer.py pyrogen_swig.py coot_git.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
Byte-compiling python modules...
pyrogen.pyatom_types.pyjay_util.pytautomer.pypyrogen_swig.pycoot_git.py
Byte-compiling python modules (optimized versions) ...
pyrogen.pyatom_types.pyjay_util.pytautomer.pypyrogen_swig.pycoot_git.py
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen'
Making install in src
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
  /bin/sh ../libtool   --mode=install install -p coot-fix-nomenclature-errors '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
libtool: warning: '../ligand/libcoot-ligand.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64'
libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-fix-nomenclature-errors /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-fix-nomenclature-errors
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 install -p coot coot-density-score-by-residue '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec'
  /bin/sh ../libtool   --mode=install install -p coot-bin coot-density-score-by-residue-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec'
libtool: warning: '../lbg/libcoot-lidia.la' has not been installed in '/usr/lib64'
libtool: warning: '../ligand/libcoot-ligand.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../goograph/libcoot-goograph.la' has not been installed in '/usr/lib64'
libtool: warning: '../libgtkgraph/libcoot-gtkgraph.la' has not been installed in '/usr/lib64'
libtool: warning: '../density-contour/libcoot-isosurface.la' has not been installed in '/usr/lib64'
libtool: warning: '../build/libcoot-cabuild.la' has not been installed in '/usr/lib64'
libtool: warning: '../skeleton/libcoot-skeleton.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/angles/libcoot-AngleInfo.la' has not been installed in '/usr/lib64'
libtool: warning: '../angles/libcoot-AngleInfo.la' has not been installed in '/usr/lib64'
libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '../high-res/libcoot-high-res.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ligand/libcoot-ligand.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64'
libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-surface/libcoot-surface.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/surface/libcoot-electrostatics.la' has not been installed in '/usr/lib64'
libtool: warning: '../surface/libcoot-electrostatics.la' has not been installed in '/usr/lib64'
libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../analysis/libcoot-analysis.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../protein_db/libcoot-protein-db.la' has not been installed in '/usr/lib64'
libtool: warning: '../cootilus/libcootilus.la' has not been installed in '/usr/lib64'
libtool: warning: '../cootaneer/libcootaneer.la' has not been installed in '/usr/lib64'
libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-bin
libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64'
libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64'
libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64'
libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64'
libtool: install: install -p .libs/coot-density-score-by-residue-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-density-score-by-residue-bin
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
 install -p coot.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot'
 install -p -m 644 crunch-model.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src'
Making install in data
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data'
 install -p -m 644 tutorial-modern.pdb rnasa-1.8-all_refmac1.mtz ligands.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data'
Making install in man
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1'
 install -p -m 644 'coot.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot.1'
 install -p -m 644 'coot-density-score-by-residue.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-density-score-by-residue.1'
 install -p -m 644 'coot-compare-dictionaries.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-compare-dictionaries.1'
 install -p -m 644 'coot-available-comp-id.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-available-comp-id.1'
 install -p -m 644 'coot-bfactan.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-bfactan.1'
 install -p -m 644 'coot-fix-nomenclature-errors.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-fix-nomenclature-errors.1'
 install -p -m 644 'coot-make-shelx-restraints.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-make-shelx-restraints.1'
 install -p -m 644 'coot-mini-rsr.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-mini-rsr.1'
 install -p -m 644 'lidia.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/lidia.1'
 install -p -m 644 'findwaters.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/findwaters.1'
 install -p -m 644 'findligand.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/findligand.1'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man'
Making install in rama-data
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/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-0.8.8-2.fc27.x86_64/usr/share/coot/rama-data'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data'
Making install in doc
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
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-0.8.8/doc'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc'
Making install in rcrane
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/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-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane'
 install -p -m 644 preLaunchCheck.py safelog.py extendChain.py reportInputErrors.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/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-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/data'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane'
Making install in pixmaps
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
Making install in icons
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons'
make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[3]: Nothing to be done for 'install-exec-am'.
for icon in hicolor_apps_48x48_coot.png hicolor_apps_64x64_coot.png hicolor_apps_96x96_coot.png hicolor_apps_256x256_coot.png hicolor_apps_scalable_coot.svg; do \
	THEME=`   echo $icon | cut -d_ -f1`; \
	CONTEXT=` echo $icon | cut -d_ -f2`; \
	SIZE=`    echo $icon | cut -d_ -f3`; \
	ICONFILE=`echo $icon | cut -d_ -f4`; \
	mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/icons/$THEME/$SIZE/$CONTEXT; \
	install -p -m 644 ./$icon /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/icons/$THEME/$SIZE/$CONTEXT/$ICONFILE; \
done;
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons'
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[3]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps'
 install -p -m 644 coot-0.8.8.png coot-0.8.7.png add-alt-conf.png dna.svg probe-clash.svg add-alt-conf.svg edit-backbone.svg radacina_handcuffs-small.svg add-peptide-1.png edit-chi.png ramachandran.png add-peptide-1.svg edit-chi.svg refine-1.svg add-water.svg emsley.jpg refine.png anchor.svg env-distances.png regularize-1.svg aniso-atom.png env-distances.svg regularize.png aniso-atom.svg eugene.jpg renumber-residues.svg appointment-new.png flip-peptide.png reset-view-32.png atom-at-pointer.png flip-peptide.svg reset-view-32.svg atom-at-pointer.svg generic-display-objects.svg reset-view.png auto-fit-rotamer.png geom.svg reset-view.svg auto-fit-rotamer.svg ghosts.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps'
 install -p -m 644 residue-info.png azerbaijan2.svg ghosts.svg residue-info.svg azerbaijan.svg gln-asn-b-factors.svg rigid-body.png calculate-ghosts.svg gln-asn-b-factorssvg.svg rigid-body.svg cell+symm.png glyco-structures.svg rotamers.png cell+symm.svg gnome-run.png rotamers.svg change-chain-id.svg go-to-atom.svg rtz.png chiral.png go-to-ligand.svg rtz.svg chiral.svg gtk-connect-16.png scroll-wheel.svg connect-to-ccp4.svg gtk-font.png secondary-structure.svg connect-to-oca.svg gtk-open-16.png sequence-view.png connect-to-usf.svg gtk-open-24.png sequence-view.svg connect-to-world.svg gtk-open.png side-chain-180.png kevin.jpg side-chain-180.svg kevin-orig.jpg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps'
 install -p -m 644 smiles.png kleywegt.svg smiles.svg map.svg spin-view.png coot-favicon.png merge-molecules.svg spin-view.svg coot-icon.png mutate-auto-fit.svg stereo-view.svg coot-save.png mutate.svg stop.svg coot-save-symm.png panel-screenshot.png temperature.png crosshairs.png peptide-omega.png temperature.svg crosshairs.svg peptide-omega.svg torsion-general.svg delete.png phenixed.svg undo-1.png delete.svg pink-pointer.png undo-1.svg density-fit.svg pink-pointer.svg unknown-blob.png diff-map.png plane-distances.png unknown-blob.svg diff-map.svg plane-distances.svg water-diff-map.svg display-manager.png pointer-distances.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps'
 install -p -m 644 water-drop.svg display-manager.svg pointer-distances.svg koppi-green-tick-64.png rygle-red-cross-64.png forest51690-dwcheckno-incomplete-64.png go-to-ligand.png go-to-atom.png azerbaijan.png add-water.png mutate.png mutate-auto-fit.png edit-backbone.png torsion-general.png anchor.png regularize-1.png refine-1.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps'
make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps'
make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8'
 /bin/sh ./config.status
skipping
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/appdata'
 install -p -m 644 coot.appdata.xml '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/appdata'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/applications'
 install -p -m 644 coot.desktop '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/applications'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
 install -p -m 644 cootrc standard-residues.pdb colours.def mtrix-to-ncs-matrix.awk syminfo.lib '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot'
make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8'
+ mv reference-structures /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/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-0.8.8-2.fc27.x86_64/usr/bin/
+ rm -f /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.la
+ rm -f /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.la
++ find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name '*.py'
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py
+ for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py")
+ sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py
+ touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py.new
+ mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py
+ cp /builddir/build/SOURCES/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/
+ chmod 644 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py
+ desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/applications coot.desktop
+ appstream-util validate-relax --nonet /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64//usr/share/appdata/coot.appdata.xml
/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64//usr/share/appdata/coot.appdata.xml: GLib-GIO-Message: Using the 'memory' GSettings backend.  Your settings will not be saved or shared with other applications.
OK
+ /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m --build-id-seed 0.8.8-2.fc27 --unique-debug-suffix -0.8.8-2.fc27.x86_64 --unique-debug-src-base coot-0.8.8-2.fc27.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/coot-0.8.8
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-density-score-by-residue-bin
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-bin
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findwaters-bin
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findligand-bin
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/mini-rsr-bin
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-fix-nomenclature-errors
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/lidia
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-bfactan
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-available-comp-id
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-make-shelx-restraints
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-compare-dictionaries
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.so.0.0.0
extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.so.0.0.0
/usr/lib/rpm/sepdebugcrcfix: Updated 44 CRC32s, 0 CRC32s did match.
36077 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/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-0.8.8-2.fc27.x86_64/usr/lib64/python2.7 using /usr/bin/python2.7
Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/debug/usr/lib64/python2.7 using /usr/bin/python2.7
Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7 using /usr/bin/python2.7
+ /usr/lib/rpm/brp-python-hardlink
Processing files: coot-0.8.8-2.fc27.x86_64
Provides: appdata() appdata(coot.appdata.xml) application() application(coot.desktop) coot = 0.8.8-2.fc27 coot(x86-64) = 0.8.8-2.fc27
Requires(interp): /bin/sh /bin/sh /bin/sh
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /bin/sh
Requires(postun): /bin/sh
Requires(posttrans): /bin/sh
Requires: /bin/sh libAlignment.so.1()(64bit) libDataStructs.so.1()(64bit) libDepictor.so.1()(64bit) libDescriptors.so.1()(64bit) libDistGeomHelpers.so.1()(64bit) libDistGeometry.so.1()(64bit) libEigenSolvers.so.1()(64bit) libFileParsers.so.1()(64bit) libForceField.so.1()(64bit) libForceFieldHelpers.so.1()(64bit) libGL.so.1()(64bit) libGLU.so.1()(64bit) libGraphMol.so.1()(64bit) libICE.so.6()(64bit) libMolChemicalFeatures.so.1()(64bit) libMolDraw2D.so.1()(64bit) libOptimizer.so.1()(64bit) libRDGeneral.so.1()(64bit) libRDGeometryLib.so.1()(64bit) libSM.so.6()(64bit) libSmilesParse.so.1()(64bit) libSubstructMatch.so.1()(64bit) libX11.so.6()(64bit) libXmu.so.6()(64bit) libXt.so.6()(64bit) libart_lgpl_2.so.2()(64bit) libatk-1.0.so.0()(64bit) libboost_python.so.1.63.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcairo.so.2()(64bit) libccp4c.so.0()(64bit) libccp4mg-utils.so.0()(64bit) libclipper-ccp4.so.2()(64bit) libclipper-cif.so.2()(64bit) libclipper-cns.so.2()(64bit) libclipper-contrib.so.2()(64bit) libclipper-core.so.2()(64bit) libclipper-fortran.so.2()(64bit) libclipper-minimol.so.2()(64bit) libclipper-mmdb.so.2()(64bit) libclipper-phs.so.2()(64bit) libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-cabuild.so.0()(64bit) libcoot-compat.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-goograph.so.0()(64bit) libcoot-gtkgraph.so.0()(64bit) libcoot-high-res.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-isosurface.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-lidia.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-protein-db.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-skeleton.so.0()(64bit) libcoot-surface.so.0()(64bit) libcoot-utils.so.0()(64bit) libcootaneer.so.0()(64bit) libcootilus.so.0()(64bit) libcurl.so.4()(64bit) libdl.so.2()(64bit) libfontconfig.so.1()(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgdk-x11-2.0.so.0()(64bit) libgdk_pixbuf-2.0.so.0()(64bit) libgdkglext-x11-1.0.so.0()(64bit) libgio-2.0.so.0()(64bit) libglib-2.0.so.0()(64bit) libglut.so.3()(64bit) libgmodule-2.0.so.0()(64bit) libgnomecanvas-2.so.0()(64bit) libgobject-2.0.so.0()(64bit) libgoocanvas.so.3()(64bit) libgsl.so.23()(64bit) libgslcblas.so.0()(64bit) libgtk-x11-2.0.so.0()(64bit) libgtkglext-x11-1.0.so.0()(64bit) libguile.so.17()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmmdb2.so.0()(64bit) libpango-1.0.so.0()(64bit) libpangocairo-1.0.so.0()(64bit) libpangoft2-1.0.so.0()(64bit) libpangox-1.0.so.0()(64bit) libpng16.so.16()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpython2.7.so.1.0()(64bit) libsfftw.so.2()(64bit) libsrfftw.so.2()(64bit) libssm.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libutil.so.1()(64bit) rtld(GNU_HASH)
Processing files: coot-data-0.8.8-2.fc27.noarch
Provides: coot-data = 0.8.8-2.fc27
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: libcoot-0.8.8-2.fc27.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.aKDRXB
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.8.8
+ DOCDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot
+ cp -pr AUTHORS /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot
+ cp -pr README /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.G1uwxa
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.8.8
+ LICENSEDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/libcoot
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/libcoot
+ cp -pr COPYING /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/libcoot
+ exit 0
Provides: libccp4mg-utils.so.0()(64bit) libcoot = 0.8.8-2.fc27 libcoot(x86-64) = 0.8.8-2.fc27 libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-cabuild.so.0()(64bit) libcoot-compat.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-goograph.so.0()(64bit) libcoot-gtkgraph.so.0()(64bit) libcoot-high-res.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-isosurface.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-lidia.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-protein-db.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-skeleton.so.0()(64bit) libcoot-surface.so.0()(64bit) libcoot-tw.so.0()(64bit) libcoot-utils.so.0()(64bit) libcoot_py_restraints.so.0()(64bit) libcootaneer.so.0()(64bit) libcootilus.so.0()(64bit)
Requires(interp): /sbin/ldconfig /sbin/ldconfig
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires(post): /sbin/ldconfig
Requires(postun): /sbin/ldconfig
Requires: libDepictor.so.1()(64bit) libDescriptors.so.1()(64bit) libFileParsers.so.1()(64bit) libForceField.so.1()(64bit) libForceFieldHelpers.so.1()(64bit) libGL.so.1()(64bit) libGraphMol.so.1()(64bit) libMolChemicalFeatures.so.1()(64bit) libRDGeneral.so.1()(64bit) libRDGeometryLib.so.1()(64bit) libSmilesParse.so.1()(64bit) libSubstructMatch.so.1()(64bit) libboost_python.so.1.63.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcairo.so.2()(64bit) libccp4mg-utils.so.0()(64bit) libclipper-ccp4.so.2()(64bit) libclipper-contrib.so.2()(64bit) libclipper-core.so.2()(64bit) libclipper-minimol.so.2()(64bit) libclipper-mmdb.so.2()(64bit) libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-utils.so.0()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgdk-x11-2.0.so.0()(64bit) libglib-2.0.so.0()(64bit) libgobject-2.0.so.0()(64bit) libgoocanvas.so.3()(64bit) libgsl.so.23()(64bit) libgslcblas.so.0()(64bit) libgtk-x11-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmmdb2.so.0()(64bit) libpango-1.0.so.0()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpython2.7.so.1.0()(64bit) libsrfftw.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: libcoot-devel-0.8.8-2.fc27.x86_64
Provides: libcoot-devel = 0.8.8-2.fc27 libcoot-devel(x86-64) = 0.8.8-2.fc27
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libccp4mg-utils.so.0()(64bit) libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-cabuild.so.0()(64bit) libcoot-compat.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-goograph.so.0()(64bit) libcoot-gtkgraph.so.0()(64bit) libcoot-high-res.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-isosurface.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-lidia.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-protein-db.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-skeleton.so.0()(64bit) libcoot-surface.so.0()(64bit) libcoot-tw.so.0()(64bit) libcoot-utils.so.0()(64bit) libcoot_py_restraints.so.0()(64bit) libcootaneer.so.0()(64bit) libcootilus.so.0()(64bit)
Processing files: python2-coot-0.8.8-2.fc27.x86_64
Provides: python-coot = 0.8.8-2.fc27 python2-coot = 0.8.8-2.fc27 python2-coot(x86-64) = 0.8.8-2.fc27
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: libDepictor.so.1()(64bit) libGraphMol.so.1()(64bit) libRDGeneral.so.1()(64bit) libSmilesParse.so.1()(64bit) libSubstructMatch.so.1()(64bit) libboost_python.so.1.63.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcoot-analysis.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-utils.so.0()(64bit) libcoot_py_restraints.so.0()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libmmdb2.so.0()(64bit) libpython2.7.so.1.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) python(abi) = 2.7 rtld(GNU_HASH)
Obsoletes: python-coot < 0.8.8-2.fc27
Processing files: coot-doc-0.8.8-2.fc27.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Yg5QGE
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.8.8
+ DOCDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc
+ cp -pr doc/coot-keys-and-buttons.pdf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc
+ cp -pr doc/coot-user-manual.pdf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.gVXaW8
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.8.8
+ LICENSEDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/coot-doc
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/coot-doc
+ cp -pr COPYING /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/coot-doc
+ exit 0
Provides: coot-doc = 0.8.8-2.fc27
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: coot-debuginfo-0.8.8-2.fc27.x86_64
Provides: coot-debuginfo = 0.8.8-2.fc27 coot-debuginfo(x86-64) = 0.8.8-2.fc27 debuginfo(build-id) = 027a5aaefa7923b6cd4752f07f122460fbc5e846 debuginfo(build-id) = 0872039c2cdd7a33489061470aa33868e8c09838 debuginfo(build-id) = 0ef8d224ac6279f0100310435bcb6dda66e8ac27 debuginfo(build-id) = 11ffcf7ccb80df8521a01e4907ddd72b6bec65c9 debuginfo(build-id) = 1414e707aed8f5f043ce2a5df7a02f5ac6b3d17d debuginfo(build-id) = 1cb493c134e01015dafa6fd88af2b2fe23efdfc2 debuginfo(build-id) = 20de56a46a9998b56f3d3b2d119824c04c77bc55 debuginfo(build-id) = 29031d5d3f2ed295aeacd28e9d0e657ed16d47fe debuginfo(build-id) = 2dde4f97c044326ad8062e55edce0cea84c81927 debuginfo(build-id) = 427daff2bfba409e7a0a9ff4efd4b38124698383 debuginfo(build-id) = 4722e9fdc6fdd674b261f3a1c50545e7b8b0a245 debuginfo(build-id) = 476ac95e22747c7f6643eae82cf18bf03b7ea63f debuginfo(build-id) = 5213fbd0d16c1596219f5a7e55e57bd75af1408f debuginfo(build-id) = 5642cb0e642ce20c0e91bd019ef78425f7cc31ea debuginfo(build-id) = 591ab8f5bbf97b1107660d5643d3061af8a16e2d debuginfo(build-id) = 5b946207603ca562491a9c4e0eeb9b63651a299d debuginfo(build-id) = 5d46f688759cdf18ac8723e061ed99345d929a13 debuginfo(build-id) = 62463d53d06ee1d351ef7d87a0e586b73b97d92e debuginfo(build-id) = 62a941922bce29692b148905438de196e20809d6 debuginfo(build-id) = 63bdc5894a88ed337b36dfc97fa460fe4beeaac4 debuginfo(build-id) = 77d7d335bb6373f68d62a183cdc1ec628a354149 debuginfo(build-id) = 85b67d5a15b69b7be9fec46b31ad292a4b48dac2 debuginfo(build-id) = 894ddf3905a3337a1368e2668186225f409074f1 debuginfo(build-id) = 8d2691be55afe0df28f632f463d4ad817cb184e0 debuginfo(build-id) = 8eb17ebf166f6f4ebb00848eb21726c00ad2251e debuginfo(build-id) = a2be31a2d09630871437d5e47584ba8a4dfee09a debuginfo(build-id) = a690479d5e409236c2c2689e958079e563207959 debuginfo(build-id) = a7bbf1fac3297d90cf2e90d09e557a31aa1b2adb debuginfo(build-id) = a96c717d0811090a92cb6f1160b9035374cef196 debuginfo(build-id) = b3487130405ceae3552dcd77f957df0f5f8e15de debuginfo(build-id) = b425e72ff137d912728734ec596303c8be050642 debuginfo(build-id) = b56e5e35887b2c522bd63645f1587e0e3ad65bfc debuginfo(build-id) = b9ff09feff53a5afbd05f205fdddcec7a00647d1 debuginfo(build-id) = c55742aa9a110f8bc784a42ae1de90dc7f3398af debuginfo(build-id) = c5b064751e2de689f392a542e5e84f9b154fb4fb debuginfo(build-id) = d147d463748bfa8b58e036404102ae3a2b04629d debuginfo(build-id) = d43998c767c60314f6483a7a4ad0ac394e70790d debuginfo(build-id) = de43bbfa9848826122f4df5fa48dff87ff941849 debuginfo(build-id) = dfdb3b75aefc0566d54cda60b9ff51b327a9c7ac debuginfo(build-id) = e1bd35b6b7ac1030c1e458758c758780bc542152 debuginfo(build-id) = e38e87ec1b1c56038eccc4f41d402b7feec30ec0 debuginfo(build-id) = e3f3fc1d7edbe7f8385648d1e8e2631cb59f9b2e debuginfo(build-id) = e8811c763435564a50bfcdf9b9197d43277f40da debuginfo(build-id) = fb058ec60e9d2b6593121cce45266b681e756032
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64
Wrote: /builddir/build/RPMS/coot-0.8.8-2.fc27.x86_64.rpm
Wrote: /builddir/build/RPMS/coot-data-0.8.8-2.fc27.noarch.rpm
Wrote: /builddir/build/RPMS/libcoot-0.8.8-2.fc27.x86_64.rpm
Wrote: /builddir/build/RPMS/libcoot-devel-0.8.8-2.fc27.x86_64.rpm
Wrote: /builddir/build/RPMS/python2-coot-0.8.8-2.fc27.x86_64.rpm
Wrote: /builddir/build/RPMS/coot-doc-0.8.8-2.fc27.noarch.rpm
Wrote: /builddir/build/RPMS/coot-debuginfo-0.8.8-2.fc27.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.8sIfXi
+ umask 022
+ cd /builddir/build/BUILD
+ cd coot-0.8.8
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64
+ exit 0
Child return code was: 0