coot Build Log

Checking out coot 2019-06-11 15:48:23.365
Configuring coot 2019-06-11 15:48:23.365
/home/ccb63/Downloads/devtools/checkout/coot/configure --prefix /opt/xtal/ccp4-7.0-linux64 --libdir '/opt/xtal/ccp4-7.0-linux64/lib' --with-enhanced-ligand-tools --with-guile --with-python --with-pygtk --with-goocanvas-prefix=/opt/xtal/ccp4-7.0-linux64 --with-guile-gtk --includedir=/opt/xtal/ccp4-7.0-linux64/include/coot RDKIT_CXXFLAGS=-I/opt/xtal/ccp4-7.0-linux64/include/rdkit RDKIT_LIBS='-lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7' COOT_BUILD_INFO_STRING='CCP4, Oxfordshire' --enable-silent-rules --enable-shared --disable-static 
configure: WARNING: unrecognized options: --enable-silent-rules
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld
checking if the linker (/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /opt/rh/devtoolset-2/root/usr/bin//nm -B
checking the name lister (/opt/rh/devtoolset-2/root/usr/bin//nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 98304
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /opt/rh/devtoolset-2/root/usr/bin//nm -B output from gcc object... ok
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 whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
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... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/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 for ld used by g++... /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld -m elf_x86_64
checking if the linker (/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/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... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which libtool initialization strategy to adopt... AC-PROG-LIBTOOL
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 pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GLIB... yes
checking if this is MINGW on Windows... no
checking for SQLite3... yes
checking for mmdb2... yes
checking for ssm... yes
no
checking for non-prefixed single-precision FFTW2 (fftw.h)... yes
checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... /opt/xtal/ccp4-7.0-linux64/bin/guile
checking for guile-config... /opt/xtal/ccp4-7.0-linux64/bin/guile-config
checking for guile-tools... /opt/xtal/ccp4-7.0-linux64/bin/guile-tools
checking libguile compile flags... -I/opt/xtal/ccp4-7.0-linux64/include  -pthread
checking libguile link flags...  -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lguile -lltdl -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -lgmp -lcrypt -lm -lltdl
checking for Guile-Lib... yes
checking for guile-gui... yes
checking GUILE_VERSION: 1.8
checking for gsl-config... /opt/xtal/ccp4-7.0-linux64/bin/gsl-config
checking for GSL - version >= 1.3... yes
checking for GTK... yes
checking for GNOME_CANVAS... yes
checking for pkg-config... /usr/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0)
checking for glLineWidth in -lGL... yes
checking for GLUT... yes
checking for Python... checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
Cool, using Python
checking for PYGTK... yes
Good we have pygtk
checking for 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}/lib/python2.7/site-packages
checking for guile-gtk... 
checking for boostlib >= 1.20.0... yes
checking for python2.7... /opt/xtal/ccp4-7.0-linux64/devbin/python
checking for a version of Python >= '2.1.0'... yes
checking for the distutils Python package... yes
checking for Python include path... -I/opt/xtal/ccp4-7.0-linux64/include/python2.7
checking for Python library path... -L/opt/xtal/ccp4-7.0-linux64/lib -lpython2.7
checking for Python site-packages path... /opt/xtal/ccp4-7.0-linux64/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 whether boost_python is the correct library... yes
checking libglade... no
checking for Goocanvas... yes
Not using MySQL database
checking for curl >= 7.9.7... 7.37.1
checking build type... Linux-x86_64-centos-5-python-gtk2
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 data/rama-coeffs/Makefile
config.status: creating data/cho-models/Makefile
config.status: creating data/cho-acedrg/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 pli/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
configure: WARNING: unrecognized options: --enable-silent-rules
Building coot 2019-06-11 15:48:41.638
make -j 1
Making all in auxil
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Making all in catcheck
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/catcheck'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/catcheck'
Making all in rama
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/rama'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/rama'
Making all in sec-str
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/sec-str'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/sec-str'
Making all in strand-analysis
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/strand-analysis'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/strand-analysis'
Making all in vectors
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/vectors'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/vectors'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
Making all in scheme
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/scheme'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/scheme'
Making all in python
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/python'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/python'
Making all in pdb-templates
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pdb-templates'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pdb-templates'
Making all in macros
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/macros'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/macros'
Making all in compat
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/compat'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/compat'
Making all in utils
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/utils'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/utils'
Making all in protein_db
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/protein_db'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/protein_db'
Making all in mini-mol
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/mini-mol'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/mini-mol'
Making all in geometry
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/geometry'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/geometry'
Making all in coot-utils
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-utils'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-utils'
Making all in surface
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/surface'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/surface'
Making all in coot-surface
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-surface'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-surface'
Making all in lidia-core
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/lidia-core'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/lidia-core'
Making all in coords
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coords'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coords'
Making all in angles
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/angles'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/angles'
Making all in skeleton
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/skeleton'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/skeleton'
Making all in ccp4mg-utils
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils'
Making all in density-contour
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/density-contour'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/density-contour'
Making all in db-main
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/db-main'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/db-main'
Making all in analysis
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/analysis'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/analysis'
Making all in ideal
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ideal'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ideal'
Making all in ligand
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ligand'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ligand'
Making all in high-res
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/high-res'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/high-res'
Making all in build
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/build'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/build'
Making all in greg-tests
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/greg-tests'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/greg-tests'
Making all in python-tests
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/python-tests'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/python-tests'
Making all in tw
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/tw'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/tw'
Making all in libgtkgraph
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/libgtkgraph'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/libgtkgraph'
Making all in lbg
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/lbg'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/lbg'
Making all in cootaneer
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/cootaneer'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/cootaneer'
Making all in cootilus
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/cootilus'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/cootilus'
Making all in goograph
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/goograph'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/goograph'
Making all in pli
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pli'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pli'
Making all in pyrogen
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
Making all in src
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/src'
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2\" -DPACKAGE_STRING=\"coot\ 0.8.9.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=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 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/home/ccb63/Downloads/devtools/checkout/coot/src  -I/home/ccb63/Downloads/devtools/checkout/coot -I/opt/xtal/ccp4-7.0-linux64/include/rdkit  -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK  -I/opt/xtal/ccp4-7.0-linux64/include  -pthread  -DHAVE_GNOME_CANVAS -pthread -I/opt/xtal/ccp4-7.0-linux64/include/libgnomecanvas-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/pango-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/gail-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/libart-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/gtk-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/gtk-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/atk-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/cairo -I/opt/xtal/ccp4-7.0-linux64/include/gdk-pixbuf-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/glib-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/glib-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/pixman-1 -I/opt/xtal/ccp4-7.0-linux64/include/freetype2 -I/opt/xtal/ccp4-7.0-linux64/include/libpng16   -DCOOT_USE_GTK2_INTERFACE  -pthread -I/opt/xtal/ccp4-7.0-linux64/include/gtkglext-1.0 -I/opt/xtal/ccp4-7.0-linux64/lib/gtkglext-1.0/include -I/opt/xtal/ccp4-7.0-linux64/include/gtk-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/gtk-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/pango-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/gdk-pixbuf-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/glib-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/glib-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/cairo -I/opt/xtal/ccp4-7.0-linux64/include/pixman-1 -I/opt/xtal/ccp4-7.0-linux64/include/freetype2 -I/opt/xtal/ccp4-7.0-linux64/include/libpng16 -I/opt/xtal/ccp4-7.0-linux64/include/atk-1.0    -DHAVE_GOOCANVAS -I/opt/xtal/ccp4-7.0-linux64/include/goocanvas-1.0 -pthread -I/opt/xtal/ccp4-7.0-linux64/include/gtk-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/gtk-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/atk-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/cairo -I/opt/xtal/ccp4-7.0-linux64/include/gdk-pixbuf-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/pango-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/glib-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/glib-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/pixman-1 -I/opt/xtal/ccp4-7.0-linux64/include/freetype2 -I/opt/xtal/ccp4-7.0-linux64/include/libpng16  -DHAVE_SSMLIB -DMMDB_HAS_LINK_DISTANCE  -I/opt/xtal/ccp4-7.0-linux64/include -DCLIPPER_HAS_TOP8000 -pthread -I/opt/xtal/ccp4-7.0-linux64/include/pygtk-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/gtk-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/libffi-3.0.13/include -I/opt/xtal/ccp4-7.0-linux64/include/glib-2.0 -I/opt/xtal/ccp4-7.0-linux64/lib/glib-2.0/include -I/opt/xtal/ccp4-7.0-linux64/lib/gtk-2.0/include -I/opt/xtal/ccp4-7.0-linux64/include/atk-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/cairo -I/opt/xtal/ccp4-7.0-linux64/include/gdk-pixbuf-2.0 -I/opt/xtal/ccp4-7.0-linux64/include/pango-1.0 -I/opt/xtal/ccp4-7.0-linux64/include/pixman-1 -I/opt/xtal/ccp4-7.0-linux64/include/freetype2 -I/opt/xtal/ccp4-7.0-linux64/include/libpng16    -DUSE_SQLITE3   -I/opt/xtal/ccp4-7.0-linux64/include                   -DPKGDATADIR='"/opt/xtal/ccp4-7.0-linux64/share/coot"' -DPACKAGE_LOCALE_DIR='"/opt/xtal/ccp4-7.0-linux64/share/coot/locale"' -DPKGPYTHONDIR='"/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot"' -DDATADIR='"/opt/xtal/ccp4-7.0-linux64/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-centos-5-python-gtk2"' -DCOOT_BUILD_INFO_STRING='"CCP4, Oxfordshire"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/opt/xtal/ccp4-7.0-linux64/include  -pthread -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYTHON -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL  -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused  -MT git-revision-count.o -MD -MP -MF .deps/git-revision-count.Tpo -c -o git-revision-count.o git-revision-count.cc
mv -f .deps/git-revision-count.Tpo .deps/git-revision-count.Po
/bin/sh ../libtool --tag=CXX   --mode=link g++ -DPKGDATADIR='"/opt/xtal/ccp4-7.0-linux64/share/coot"' -DPACKAGE_LOCALE_DIR='"/opt/xtal/ccp4-7.0-linux64/share/coot/locale"' -DPKGPYTHONDIR='"/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot"' -DDATADIR='"/opt/xtal/ccp4-7.0-linux64/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-centos-5-python-gtk2"' -DCOOT_BUILD_INFO_STRING='"CCP4, Oxfordshire"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/opt/xtal/ccp4-7.0-linux64/include  -pthread -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYTHON -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYGTK  -DHAVE_GSL  -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused   -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -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-bonds.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-curlew.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-alignment.o cc-interface-png.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-alignment.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 sequence-view.o seq-view-interface.o support.o support-gtk2-extras.o testing.o testing-2.o trackball.o user-mods.o xmap-utils.o view.o coot_wrap_python.o  ../lbg/libcoot-lidia.la ../pli/libcoot-pli.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           -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2   -L/opt/xtal/ccp4-7.0-linux64/lib -lssm -lmmdb2    -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2   -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -lguilegtk-2.0 -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lguile -lltdl -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -lgmp -lcrypt -lm -lltdl   -Wl,--export-dynamic -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0   -lglut  -lXmu -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0    -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0   -L/opt/xtal/ccp4-7.0-linux64/lib -lgsl -lgslcblas -lm  -L/opt/xtal/ccp4-7.0-linux64/lib -lcurl  -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7  -lboost_python -L/opt/xtal/ccp4-7.0-linux64/lib -lgoocanvas -L/opt/xtal/ccp4-7.0-linux64/lib -lsqlite3   -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0   
libtool: link: g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -DPACKAGE_LOCALE_DIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot/locale\" -DPKGPYTHONDIR=\"/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot\" -DDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-centos-5-python-gtk2\" "-DCOOT_BUILD_INFO_STRING=\"CCP4, Oxfordshire\"" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/opt/xtal/ccp4-7.0-linux64/include -pthread -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYTHON -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -s -Wl,--hash-style=both -Wl,--build-id=sha1 -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-bonds.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-curlew.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-alignment.o cc-interface-png.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-alignment.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 sequence-view.o seq-view-interface.o support.o support-gtk2-extras.o testing.o testing-2.o trackball.o user-mods.o xmap-utils.o view.o coot_wrap_python.o -Wl,-export-dynamic -pthread -s -Wl,--hash-style=both -Wl,--build-id=sha1 -Wl,--export-dynamic -pthread -pthread -pthread -pthread  -L/opt/xtal/ccp4-7.0-linux64/lib ../lbg/.libs/libcoot-lidia.so ../pli/.libs/libcoot-pli.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 /home/ccb63/Downloads/devtools/builddir/coot/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so ../db-main/.libs/libcoot-db-main.so ../high-res/.libs/libcoot-high-res.so /home/ccb63/Downloads/devtools/builddir/coot/ligand/.libs/libcoot-ligand.so /home/ccb63/Downloads/devtools/builddir/coot/ideal/.libs/libcoot-ideal.so /home/ccb63/Downloads/devtools/builddir/coot/db-main/.libs/libcoot-db-main.so /home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils/.libs/libccp4mg-utils.so /home/ccb63/Downloads/devtools/builddir/coot/analysis/.libs/libcoot-analysis.so ../ideal/.libs/libcoot-ideal.so /home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs/libcoot-map-heavy.so /home/ccb63/Downloads/devtools/builddir/coot/coords/.libs/libcoot-coords.so /home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs/libcoot-shelx.so /home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs/libcoot-lidia-core.so ../coot-surface/.libs/libcoot-surface.so /home/ccb63/Downloads/devtools/builddir/coot/surface/.libs/libcoot-electrostatics.so ../surface/.libs/libcoot-electrostatics.so -lrfftw -lfftw ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-heavy.so /home/ccb63/Downloads/devtools/builddir/coot/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 /home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs/libcoot-coord-utils.so /home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs/libcoot-geometry.so /home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs/libcoot-mini-mol.so /home/ccb63/Downloads/devtools/builddir/coot/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-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lssm -lmmdb2 -lpthread -ldl -lutil -lguilegtk-2.0 -lguile -lgmp -lcrypt -lltdl -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXt -lSM -lICE -lpangox-1.0 -lX11 -lglut -lXmu -lgnomecanvas-2 -lart_lgpl_2 -lgsl -lgslcblas -lm -lcurl -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lpython2.7 -lboost_python -lgoocanvas -lsqlite3 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -pthread -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/src'
Making all in data
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Making all in rama-coeffs
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/rama-coeffs'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/rama-coeffs'
Making all in cho-models
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-models'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-models'
Making all in cho-acedrg
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-acedrg'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-acedrg'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
Making all in man
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/man'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/man'
Making all in rama-data
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/rama-data'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/rama-data'
Making all in doc
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/doc'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/doc'
Making all in rcrane
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/rcrane'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/rcrane'
Making all in pixmaps
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Making all in icons
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps/icons'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps/icons'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Installing coot 2019-06-11 15:48:52.724
make install DESTDIR=/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot
Making install in auxil
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Making install in catcheck
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/catcheck'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/catcheck'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/catcheck'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/catcheck'
Making install in rama
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/rama'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/rama'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/rama'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/rama'
Making install in sec-str
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/sec-str'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/sec-str'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/sec-str'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/sec-str'
Making install in strand-analysis
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/strand-analysis'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/strand-analysis'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/strand-analysis'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/strand-analysis'
Making install in vectors
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/vectors'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/vectors'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/vectors'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil/vectors'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/auxil'
Making install in scheme
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/scheme'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/scheme'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/scheme" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/scheme"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/scheme/0-auto-rot.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/coot-utils.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/get-ebi.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/mutate.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/background-demo.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/demo-script.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/gtkin.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/my-readline.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/bit.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/extra-top-level.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/hello.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/raster3d.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/brute-lsqman.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/file-utils.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/junk.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/refmac.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/coot-gui.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/filter.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/libcheck.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/simple.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/coot.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/get-ebi.save.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/local-code.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/trivial.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/gap.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/remote-control.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/povray.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/coot-lsq.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/shelx.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/group-settings.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/fitting.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/americanisms.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/tips.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/tips-gui.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/generic-objects.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/cns2coot.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/extensions.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/ncs.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/create-server.scsh /home/ccb63/Downloads/devtools/checkout/coot/scheme/coot-crash-catcher.scm '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/scheme'
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/scheme/snarf-coot-docs.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/clear-backup.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/bones-reader.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/matrices.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/fascinating-things.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/shelx-extensions.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/parse-pisa-xml.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/check-for-updates.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/3d-generator-import.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/gui-hole.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/gui-prosmart.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/get-recent-pdbe.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/json-reader.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/jligand.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/jligand-gui.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/redefine-functions.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/user-define-restraints.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/template-key-bindings.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/gui-add-linked-cho.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/ligand-check.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/run-mogul.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/contact-score-isolated-ligand.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/enhanced-ligand.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/gui-ligand-sliders.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/dictionary-generators.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/cho-restraints-from-models.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/interactive-nudge-residues.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/acedrg-link.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/add-linked-cho.scm /home/ccb63/Downloads/devtools/checkout/coot/scheme/find-baddies.scm '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/scheme'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/scheme'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/scheme'
Making install in python
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/python'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/python'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/python/coot_utils.py /home/ccb63/Downloads/devtools/checkout/coot/python/get_ebi.py /home/ccb63/Downloads/devtools/checkout/coot/python/mutate.py /home/ccb63/Downloads/devtools/checkout/coot/python/background_demo.py /home/ccb63/Downloads/devtools/checkout/coot/python/hello.py /home/ccb63/Downloads/devtools/checkout/coot/python/raster3d.py /home/ccb63/Downloads/devtools/checkout/coot/python/brute_lsqman.py /home/ccb63/Downloads/devtools/checkout/coot/python/refmac.py /home/ccb63/Downloads/devtools/checkout/coot/python/coot_gui.py /home/ccb63/Downloads/devtools/checkout/coot/python/filter.py /home/ccb63/Downloads/devtools/checkout/coot/python/libcheck.py coot_load_modules.py /home/ccb63/Downloads/devtools/checkout/coot/python/local_code.py /home/ccb63/Downloads/devtools/checkout/coot/python/gap.py /home/ccb63/Downloads/devtools/checkout/coot/python/remote_control.py /home/ccb63/Downloads/devtools/checkout/coot/python/povray.py /home/ccb63/Downloads/devtools/checkout/coot/python/coot_lsq.py /home/ccb63/Downloads/devtools/checkout/coot/python/shelx.py /home/ccb63/Downloads/devtools/checkout/coot/python/group_settings.py /home/ccb63/Downloads/devtools/checkout/coot/python/fitting.py /home/ccb63/Downloads/devtools/checkout/coot/python/americanisms.py /home/ccb63/Downloads/devtools/checkout/coot/python/tips.py /home/ccb63/Downloads/devtools/checkout/coot/python/tips_gui.py /home/ccb63/Downloads/devtools/checkout/coot/python/generic_objects.py /home/ccb63/Downloads/devtools/checkout/coot/python/cns2coot.py /home/ccb63/Downloads/devtools/checkout/coot/python/extensions.py /home/ccb63/Downloads/devtools/checkout/coot/python/ncs.py /home/ccb63/Downloads/devtools/checkout/coot/python/create_server.py /home/ccb63/Downloads/devtools/checkout/coot/python/python_coot_docs.py /home/ccb63/Downloads/devtools/checkout/coot/python/clear_backup.py /home/ccb63/Downloads/devtools/checkout/coot/python/bones_reader.py /home/ccb63/Downloads/devtools/checkout/coot/python/shelx_extensions.py /home/ccb63/Downloads/devtools/checkout/coot/python/parse_pisa_xml.py /home/ccb63/Downloads/devtools/checkout/coot/python/check_for_updates.py /home/ccb63/Downloads/devtools/checkout/coot/python/3d_generator_import.py /home/ccb63/Downloads/devtools/checkout/coot/python/gui_hole.py /home/ccb63/Downloads/devtools/checkout/coot/python/gui_prosmart.py /home/ccb63/Downloads/devtools/checkout/coot/python/get_recent_pdbe.py /home/ccb63/Downloads/devtools/checkout/coot/python/jligand.py /home/ccb63/Downloads/devtools/checkout/coot/python/jligand_gui.py '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot'
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/python/redefine_functions.py /home/ccb63/Downloads/devtools/checkout/coot/python/user_define_restraints.py /home/ccb63/Downloads/devtools/checkout/coot/python/template_key_bindings.py /home/ccb63/Downloads/devtools/checkout/coot/python/gui_add_linked_cho.py /home/ccb63/Downloads/devtools/checkout/coot/python/ligand_check.py /home/ccb63/Downloads/devtools/checkout/coot/python/run_mogul.py /home/ccb63/Downloads/devtools/checkout/coot/python/contact_score_isolated_ligand.py /home/ccb63/Downloads/devtools/checkout/coot/python/gui_contact_score_isolated_ligand.py /home/ccb63/Downloads/devtools/checkout/coot/python/enhanced_ligand.py /home/ccb63/Downloads/devtools/checkout/coot/python/gui_ligand_sliders.py /home/ccb63/Downloads/devtools/checkout/coot/python/dictionary_generators.py /home/ccb63/Downloads/devtools/checkout/coot/python/cho_restraints_from_models.py /home/ccb63/Downloads/devtools/checkout/coot/python/interactive_nudge_residues.py /home/ccb63/Downloads/devtools/checkout/coot/python/acedrg_link.py /home/ccb63/Downloads/devtools/checkout/coot/python/coot_toolbuttons.py /home/ccb63/Downloads/devtools/checkout/coot/python/rcrane_loader.py /home/ccb63/Downloads/devtools/checkout/coot/python/add_linked_cho.py /home/ccb63/Downloads/devtools/checkout/coot/python/find_baddies.py /home/ccb63/Downloads/devtools/checkout/coot/python/pdbe_validation_data.py /home/ccb63/Downloads/devtools/checkout/coot/python/ligand_validation_sliders.py /home/ccb63/Downloads/devtools/checkout/coot/python/chemical_feature_clusters.py /home/ccb63/Downloads/devtools/checkout/coot/python/res_spec_utils.py /home/ccb63/Downloads/devtools/checkout/coot/python/coot_output_to_window.py '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/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.pycho_restraints_from_models.pyinteractive_nudge_residues.pyacedrg_link.pycoot_toolbuttons.pyrcrane_loader.pyadd_linked_cho.pyfind_baddies.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.pycoot_output_to_window.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.pycho_restraints_from_models.pyinteractive_nudge_residues.pyacedrg_link.pycoot_toolbuttons.pyrcrane_loader.pyadd_linked_cho.pyfind_baddies.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.pycoot_output_to_window.py
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/python'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/python'
Making install in pdb-templates
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pdb-templates'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pdb-templates'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/ASN-NAG-via-NAG-ASN.pdb /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/pyranose-pyranose-via-BETA1-4.pdb /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/pyranose-pyranose-via-ALPHA1-2.pdb /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/pyranose-pyranose-via-ALPHA1-3.pdb /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/pyranose-pyranose-via-ALPHA1-6.pdb /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/SIA-pyranose-via-ALPHA2-3.pdb /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-ALPHA1-2.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-ALPHA1-3.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-FUC-core-ALPHA1-3.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-FUC-core-ALPHA1-2.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-FUC-core-ALPHA1-6.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-NAG-core-NAG-SER.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-ALPHA1-6.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-ALPHA2-3.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-BETA1-2.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-BETA1-3.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-BETA1-4.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-BETA1-6.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-NAG-ASN.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/link-by-torsion-to-pyranose-core-XYP-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/NAG-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/BMA-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/MAN-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/GLC-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/GAL-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/FUC-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/FUL-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/XYP-decorations.tab /home/ccb63/Downloads/devtools/checkout/coot/pdb-templates/theor-helix-70.pdb '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pdb-templates'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pdb-templates'
Making install in macros
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/macros'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/macros'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/macros'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/macros'
Making install in compat
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/compat'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/compat'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-compat.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-compat.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-compat.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so.0 || { rm -f libcoot-compat.so.0 && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so || { rm -f libcoot-compat.so && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-compat.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-compat.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/compat" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/compat"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/compat/coot-getopt.h /home/ccb63/Downloads/devtools/checkout/coot/compat/coot-sysdep.h /home/ccb63/Downloads/devtools/checkout/coot/compat/getopt_int.h /home/ccb63/Downloads/devtools/checkout/coot/compat/sleep-fixups.h '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/compat'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/compat'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/compat'
Making install in utils
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/utils'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/utils'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-utils.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-utils.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-utils.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so.0 || { rm -f libcoot-utils.so.0 && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so || { rm -f libcoot-utils.so && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-utils.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-utils.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/utils" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/utils"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/utils/coot-utils.hh /home/ccb63/Downloads/devtools/checkout/coot/utils/coot-fasta.hh /home/ccb63/Downloads/devtools/checkout/coot/utils/dodec.hh /home/ccb63/Downloads/devtools/checkout/coot/utils/win-compat.hh /home/ccb63/Downloads/devtools/checkout/coot/utils/ctpl_stl.h /home/ccb63/Downloads/devtools/checkout/coot/utils/pir-alignment.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/utils'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/utils'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/utils'
Making install in protein_db
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/protein_db'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/protein_db'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-protein-db.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-protein-db.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-protein-db.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0 || { rm -f libcoot-protein-db.so.0 && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so || { rm -f libcoot-protein-db.so && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-protein-db.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-protein-db.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/protein_db" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/protein_db"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/protein_db/protein_db.h /home/ccb63/Downloads/devtools/checkout/coot/protein_db/protein_db_utils.h /home/ccb63/Downloads/devtools/checkout/coot/protein_db/rna_db.h '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/protein_db'
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/protein_db" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/protein_db"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/protein_db/protein.db '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/protein_db'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/protein_db'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/protein_db'
Making install in mini-mol
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/mini-mol'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/mini-mol'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-mini-mol.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-mini-mol.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/mini-mol; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-mini-mol.la -rpath /opt/xtal/ccp4-7.0-linux64/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-mini-mol.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0 || { rm -f libcoot-mini-mol.so.0 && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so || { rm -f libcoot-mini-mol.so && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-mini-mol.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/mini-mol" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/mini-mol"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/mini-mol/mini-mol.hh /home/ccb63/Downloads/devtools/checkout/coot/mini-mol/mini-mol-utils.hh /home/ccb63/Downloads/devtools/checkout/coot/mini-mol/atom-quads.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/mini-mol'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/mini-mol'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/mini-mol'
Making install in geometry
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/geometry'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/geometry'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-geometry.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-geometry.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/geometry; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share\" -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-geometry.la -rpath /opt/xtal/ccp4-7.0-linux64/lib 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 -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-geometry.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-geometry.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so.0 || { rm -f libcoot-geometry.so.0 && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so || { rm -f libcoot-geometry.so && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-geometry.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-geometry.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c coot-compare-dictionaries coot-make-shelx-restraints coot-available-comp-id '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
libtool: install: /usr/bin/install -c .libs/coot-compare-dictionaries /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin/coot-compare-dictionaries
libtool: install: /usr/bin/install -c .libs/coot-make-shelx-restraints /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin/coot-make-shelx-restraints
libtool: install: /usr/bin/install -c .libs/coot-available-comp-id /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin/coot-available-comp-id
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/geometry" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/geometry"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/geometry/protein-geometry.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/read-sbase.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/lbg-graph.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/srs-interface.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/dict-utils.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/dict-mismatches.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/energy-lib.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/match-results.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/hb-types.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/main-chain.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/residue-and-atom-specs.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/chem_mods.hh /home/ccb63/Downloads/devtools/checkout/coot/geometry/mol-utils-2.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/geometry'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/geometry'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/geometry'
Making install in coot-utils
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-utils'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-utils'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-coord-utils.la libcoot-shelx.la libcoot-coord-extras.la libcoot-map-utils.la libcoot-map-heavy.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-coord-utils.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coot-utils; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-coord-utils.la -rpath /opt/xtal/ccp4-7.0-linux64/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo glyco-torsions.lo coot-least-squares.lo atom-overlaps.lo reduce.lo secondary-structure-headers.lo plane-utils.lo ../geometry/libcoot-geometry.la -L/opt/xtal/ccp4-7.0-linux64/lib -lgsl -lgslcblas -lm -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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 .libs/secondary-structure-headers.o .libs/plane-utils.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coord-utils.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0 || { rm -f libcoot-coord-utils.so.0 && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so || { rm -f libcoot-coord-utils.so && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coord-utils.la
libtool: install: warning: relinking `libcoot-shelx.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coot-utils; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-shelx.la -rpath /opt/xtal/ccp4-7.0-linux64/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/coot-shelx-ins.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-shelx.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-shelx.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so.0 || { rm -f libcoot-shelx.so.0 && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so || { rm -f libcoot-shelx.so && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-shelx.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-shelx.la
libtool: install: warning: relinking `libcoot-coord-extras.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coot-utils; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-coord-extras.la -rpath /opt/xtal/ccp4-7.0-linux64/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo libcoot-coord-utils.la -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coord-extras.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0 || { rm -f libcoot-coord-extras.so.0 && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so || { rm -f libcoot-coord-extras.so && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coord-extras.la
libtool: install: warning: relinking `libcoot-map-utils.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coot-utils; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-map-utils.la -rpath /opt/xtal/ccp4-7.0-linux64/lib coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo libcoot-coord-utils.la -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lgsl -lgslcblas -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-map-utils.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0 || { rm -f libcoot-map-utils.so.0 && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so || { rm -f libcoot-map-utils.so && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-map-utils.la
libtool: install: warning: relinking `libcoot-map-heavy.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coot-utils; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-map-heavy.la -rpath /opt/xtal/ccp4-7.0-linux64/lib coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la -L/opt/xtal/ccp4-7.0-linux64/lib -lgsl -lgslcblas -lm -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/coot-map-heavy.o .libs/coot-fffear.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-map-utils -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-map-heavy.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0 || { rm -f libcoot-map-heavy.so.0 && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so || { rm -f libcoot-map-heavy.so && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-map-heavy.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/coot-utils" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/coot-utils"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/peak-search.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-trim.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-coord-utils.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-map-utils.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-coord-extras.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-map-heavy.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-lsq-types.h /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-shelx.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-rama.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/xmap-stats.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-h-bonds.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/lsq-improve.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-hole.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/read-sm-cif.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/bonded-pairs.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/tree.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/helix-analysis.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/elastic.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/emma.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/glyco-torsions.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-least-squares.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/coot-density-stats.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/atom-overlaps.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/reduce.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/secondary-structure-headers.hh /home/ccb63/Downloads/devtools/checkout/coot/coot-utils/plane-utils.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/coot-utils'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-utils'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-utils'
Making install in surface
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/surface'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/surface'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-electrostatics.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-electrostatics.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-electrostatics.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { 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 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { 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: /usr/bin/install -c .libs/libcoot-electrostatics.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-electrostatics.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/surface'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/surface'
Making install in coot-surface
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-surface'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-surface'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-surface.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-surface.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coot-surface; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-surface.la -rpath /opt/xtal/ccp4-7.0-linux64/lib coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -lglut -lXmu -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -lGL -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/coot-surface.o .libs/rgbreps.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-electrostatics -lrfftw -lfftw -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -lGL -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -pthread   -pthread -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-surface.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-surface.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so.0 || { rm -f libcoot-surface.so.0 && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so || { rm -f libcoot-surface.so && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-surface.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-surface.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-surface'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coot-surface'
Making install in lidia-core
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/lidia-core'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/lidia-core'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-lidia-core.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-lidia-core.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/lidia-core; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-lidia-core.la -rpath /opt/xtal/ccp4-7.0-linux64/lib 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 atom-types.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -L/opt/xtal/ccp4-7.0-linux64/lib -lsqlite3 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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 .libs/atom-types.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lsqlite3 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-lidia-core.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-lidia-core.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0 || { rm -f libcoot-lidia-core.so.0 && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so || { rm -f libcoot-lidia-core.so && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-lidia-core.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-lidia-core.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/lidia-core" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/lidia-core"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/lbg-shared.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/lbg-molfile.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/lig-build.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/rdkit-interface.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/use-rdkit.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/cod-types.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/neighbour-sorter.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/bond-record-container-t.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/bond-table-record-t.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/cod-atom-types.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/cod-atom-type-t.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/primes.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/chemical-feature-clusters.hh /home/ccb63/Downloads/devtools/checkout/coot/lidia-core/third-neighbour-info-t.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/lidia-core'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/lidia-core'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/lidia-core'
Making install in coords
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coords'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/coords'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-coords.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-coords.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/coords; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -DDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-coords.la -rpath /opt/xtal/ccp4-7.0-linux64/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo phenix-geo.lo phenix-geo-bonds.lo loop-path.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 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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 .libs/loop-path.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lgsl -lgslcblas -lsqlite3 -lcoot-utils -lmmdb2 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-coords.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coords.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so.0 || { rm -f libcoot-coords.so.0 && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so || { rm -f libcoot-coords.so && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-coords.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coords.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/coords" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/coords"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/coords/Bond_lines.h /home/ccb63/Downloads/devtools/checkout/coot/coords/Cartesian.h /home/ccb63/Downloads/devtools/checkout/coot/coords/cos-sin.h /home/ccb63/Downloads/devtools/checkout/coot/coords/mmdb.h /home/ccb63/Downloads/devtools/checkout/coot/coords/mmdb-extras.h /home/ccb63/Downloads/devtools/checkout/coot/coords/utils.h /home/ccb63/Downloads/devtools/checkout/coot/coords/mmdb-crystal.h /home/ccb63/Downloads/devtools/checkout/coot/coords/Bond_lines_ext.h /home/ccb63/Downloads/devtools/checkout/coot/coords/coot-close.hh /home/ccb63/Downloads/devtools/checkout/coot/coords/phenix-geo.hh /home/ccb63/Downloads/devtools/checkout/coot/coords/ramachandran-container.hh /home/ccb63/Downloads/devtools/checkout/coot/coords/loop-path.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/coords'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coords'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/coords'
Making install in angles
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/angles'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/angles'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-AngleInfo.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-AngleInfo.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0 || { rm -f libcoot-AngleInfo.so.0 && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so || { rm -f libcoot-AngleInfo.so && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-AngleInfo.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/angles" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/angles"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/angles/AngleInfo.h /home/ccb63/Downloads/devtools/checkout/coot/angles/ncube.h /home/ccb63/Downloads/devtools/checkout/coot/angles/wrapped-ncube.h '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/angles'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/angles'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/angles'
Making install in skeleton
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/skeleton'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/skeleton'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-skeleton.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-skeleton.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/skeleton; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-skeleton.la -rpath /opt/xtal/ccp4-7.0-linux64/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-AngleInfo -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lsqlite3 -lcoot-utils -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-skeleton.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0 || { rm -f libcoot-skeleton.so.0 && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so || { rm -f libcoot-skeleton.so && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-skeleton.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/skeleton" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/skeleton"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/skeleton/graphical_skel.h /home/ccb63/Downloads/devtools/checkout/coot/skeleton/dm-utils.h /home/ccb63/Downloads/devtools/checkout/coot/skeleton/BuildCas.h '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/skeleton'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/skeleton'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/skeleton'
Making install in ccp4mg-utils
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libccp4mg-utils.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libccp4mg-utils.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0 || { rm -f libccp4mg-utils.so.0 && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so || { rm -f libccp4mg-utils.so && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so; }; })
libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libccp4mg-utils.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ccp4mg-utils" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ccp4mg-utils"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/ccp4mg-utils/geomutil.h /home/ccb63/Downloads/devtools/checkout/coot/ccp4mg-utils/mgtree.h /home/ccb63/Downloads/devtools/checkout/coot/ccp4mg-utils/cartesian.h /home/ccb63/Downloads/devtools/checkout/coot/ccp4mg-utils/matrix.h /home/ccb63/Downloads/devtools/checkout/coot/ccp4mg-utils/quat.h /home/ccb63/Downloads/devtools/checkout/coot/ccp4mg-utils/ppmutil.h '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ccp4mg-utils'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils'
Making install in density-contour
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/density-contour'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/density-contour'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-isosurface.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-isosurface.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/density-contour; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-isosurface.la -rpath /opt/xtal/ccp4-7.0-linux64/lib Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lsqlite3 -lcoot-utils -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-isosurface.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0 || { rm -f libcoot-isosurface.so.0 && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so || { rm -f libcoot-isosurface.so && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-isosurface.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/density-contour" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/density-contour"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/density-contour/Vectors.h /home/ccb63/Downloads/devtools/checkout/coot/density-contour/CIsoSurface.h /home/ccb63/Downloads/devtools/checkout/coot/density-contour/density-contour-triangles.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/density-contour'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/density-contour'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/density-contour'
Making install in db-main
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/db-main'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/db-main'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-db-main.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-db-main.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/db-main; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -DDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-db-main.la -rpath /opt/xtal/ccp4-7.0-linux64/lib 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 -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/db-main.o .libs/db-strands.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-db-main.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-db-main.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so.0 || { rm -f libcoot-db-main.so.0 && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so || { rm -f libcoot-db-main.so && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-db-main.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-db-main.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/db-main" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/db-main"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/db-main/db-main.hh /home/ccb63/Downloads/devtools/checkout/coot/db-main/db-strands.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/db-main'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/db-main'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/db-main'
Making install in analysis
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/analysis'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/analysis'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-analysis.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-analysis.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/analysis; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-analysis.la -rpath /opt/xtal/ccp4-7.0-linux64/lib bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo typed-distances.lo b-factor-histogram.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lgsl -lgslcblas -lm -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.o .libs/typed-distances.o .libs/b-factor-histogram.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lcoot-utils -lmmdb2 -lgsl -lgslcblas -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-analysis.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-analysis.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so.0 || { rm -f libcoot-analysis.so.0 && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so || { rm -f libcoot-analysis.so && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-analysis.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-analysis.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c coot-bfactan '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
libtool: install: /usr/bin/install -c .libs/coot-bfactan /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin/coot-bfactan
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/analysis" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/analysis"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/analysis/bfkurt.hh /home/ccb63/Downloads/devtools/checkout/coot/analysis/mogul-interface.hh /home/ccb63/Downloads/devtools/checkout/coot/analysis/stats.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/analysis'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/analysis'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/analysis'
Making install in ideal
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ideal'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ideal'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-ideal.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-ideal.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/ideal; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -I/opt/xtal/ccp4-7.0-linux64/include -DCLIPPER_HAS_TOP8000 -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-ideal.la -rpath /opt/xtal/ccp4-7.0-linux64/lib 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 write-png.lo zo-rama.lo crankshaft.lo phi-psi.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 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lgsl -lgslcblas -lm -lpng -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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 .libs/write-png.o .libs/zo-rama.o .libs/crankshaft.o .libs/phi-psi.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -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 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lsqlite3 -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lpng -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-ideal.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-ideal.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so.0 || { rm -f libcoot-ideal.so.0 && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so || { rm -f libcoot-ideal.so && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-ideal.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-ideal.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
 /usr/bin/install -c /home/ccb63/Downloads/devtools/checkout/coot/ideal/coot-mini-rsr '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
test -z "/opt/xtal/ccp4-7.0-linux64/libexec" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c mini-rsr-bin '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec'
libtool: install: /usr/bin/install -c .libs/mini-rsr-bin /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/mini-rsr-bin
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ideal" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ideal"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/ideal/test-indexing.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/simple-restraint.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/pepflip.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/regularize-minimol.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/lograma.h /home/ccb63/Downloads/devtools/checkout/coot/ideal/zo-rama.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/phi-psi.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/parallel-planes.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/torsion-bonds.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/extra-restraints.hh /home/ccb63/Downloads/devtools/checkout/coot/ideal/model-bond-deltas.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ideal'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ideal'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ideal'
Making install in ligand
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ligand'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/ligand'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-ligand.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-ligand.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/ligand; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -DUSE_SQLITE3 -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-ligand.la -rpath /opt/xtal/ccp4-7.0-linux64/lib ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo 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 -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lsqlite3 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/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   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coords/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lsqlite3 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-ligand.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-ligand.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so.0 || { rm -f libcoot-ligand.so.0 && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so || { rm -f libcoot-ligand.so && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-ligand.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-ligand.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
 /usr/bin/install -c /home/ccb63/Downloads/devtools/checkout/coot/ligand/findwaters /home/ccb63/Downloads/devtools/checkout/coot/ligand/findligand '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
test -z "/opt/xtal/ccp4-7.0-linux64/libexec" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c findligand-bin findwaters-bin coot-make-ligands-db '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec'
libtool: install: /usr/bin/install -c .libs/findligand-bin /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/findligand-bin
libtool: install: /usr/bin/install -c .libs/findwaters-bin /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/findwaters-bin
libtool: install: /usr/bin/install -c .libs/coot-make-ligands-db /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/coot-make-ligands-db
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/data" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/ligand/ligands-2016.db '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ligand" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ligand"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/ligand/ligand.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/residue_by_phi_psi.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/wligand.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/monomer-utils.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/chi-angles.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/dunbrack.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/helix-placement.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/fast-ss-search.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/rigid-body.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/ideal-rna.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/rotamer.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/richardson-rotamer.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/torsion-general.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/primitive-chi-angles.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/dipole.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/base-pairing.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/backrub-rotamer.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/trace.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/multi-peptide.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/ligands-db.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/scored-coord.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/ligand-score-card.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/scored-molecule.hh /home/ccb63/Downloads/devtools/checkout/coot/ligand/map-point-cluster.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/ligand'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ligand'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/ligand'
Making install in high-res
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/high-res'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/high-res'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-high-res.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-high-res.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/high-res; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DHAVE_GSL -I/opt/xtal/ccp4-7.0-linux64/include -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-high-res.la -rpath /opt/xtal/ccp4-7.0-linux64/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/ideal/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/db-main/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/ccp4mg-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coords/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/analysis/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-ligand -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lsqlite3 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-high-res.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-high-res.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so.0 || { rm -f libcoot-high-res.so.0 && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so || { rm -f libcoot-high-res.so && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-high-res.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-high-res.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/high-res" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/high-res"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/high-res/high-res.hh /home/ccb63/Downloads/devtools/checkout/coot/high-res/coot-atom-graph.hh /home/ccb63/Downloads/devtools/checkout/coot/high-res/coot-node-info.hh /home/ccb63/Downloads/devtools/checkout/coot/high-res/sequence-assignment.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/high-res'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/high-res'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/high-res'
Making install in build
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/build'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/build'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-cabuild.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-cabuild.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/build; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-cabuild.la -rpath /opt/xtal/ccp4-7.0-linux64/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/CalphaBuild.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-AngleInfo -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-cabuild.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0 || { rm -f libcoot-cabuild.so.0 && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so || { rm -f libcoot-cabuild.so && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-cabuild.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/build" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/build"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/build/CalphaBuild.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/build'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/build'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/build'
Making install in greg-tests
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/greg-tests'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/greg-tests'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/greg-tests'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/greg-tests'
Making install in python-tests
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/python-tests'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/python-tests'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/python-tests'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/python-tests'
Making install in tw
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/tw'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/tw'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-tw.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-tw.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-tw.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so.0 || { rm -f libcoot-tw.so.0 && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so || { rm -f libcoot-tw.so && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-tw.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-tw.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/tw" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/tw"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/tw/coot-tw.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/tw'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/tw'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/tw'
Making install in libgtkgraph
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/libgtkgraph'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/libgtkgraph'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-gtkgraph.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcoot-gtkgraph.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-gtkgraph.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0 || { rm -f libcoot-gtkgraph.so.0 && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so || { rm -f libcoot-gtkgraph.so && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-gtkgraph.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-gtkgraph.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/libgtkgraph'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/libgtkgraph'
Making install in lbg
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/lbg'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/lbg'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-lidia.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-lidia.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/lbg; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-lidia.la -rpath /opt/xtal/ccp4-7.0-linux64/lib lbg.lo lbg-flev.lo wmolecule.lo lbg-search.lo residue-circles.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 -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lgsl -lgslcblas -lm -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lboost_python -L/opt/xtal/ccp4-7.0-linux64/lib -lgoocanvas -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/lbg.o .libs/lbg-flev.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o .libs/qed-properties.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lsqlite3 -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -lpython2.7 -lpthread -ldl -lutil -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -pthread -Wl,-export-dynamic   -pthread -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-lidia.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-lidia.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so.0 || { rm -f libcoot-lidia.so.0 && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so || { rm -f libcoot-lidia.so && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-lidia.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-lidia.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c lidia '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
libtool: install: /usr/bin/install -c .libs/lidia /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin/lidia
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/lbg/3-c-new.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/6-c-shadow-experiment.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/single.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/3-c-other.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/6-c.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/sp3.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/3-c.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/7-c.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/stereo-out.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/4-c.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/8-c.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/TheStructorr_magnifying_glass-32.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/5-c.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/Anonymous_Architetto_--_Chiave.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/TheStructorr_magnifying_glass.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/6-c-arom.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/charge.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/triple.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/6-c-exp-2.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/double.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/Trash-hydrogens-Andy_Trash_Can.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/face-smile.svg /home/ccb63/Downloads/devtools/checkout/coot/lbg/05_Hotel_Icon_Hair_Salon.svg '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps'
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/lidia" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/lidia"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/lbg/__init__.py /home/ccb63/Downloads/devtools/checkout/coot/lbg/fetch.py '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/lidia'
Byte-compiling python modules...
__init__.pyfetch.py
Byte-compiling python modules (optimized versions) ...
__init__.pyfetch.py
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/lbg" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/lbg"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/lbg/lbg.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/w-atom.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/w-bond.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/wmolecule.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/topological-equivalence.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/graphics-c-interface-functions.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/lbg-drag-and-drop.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/qed-interface.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/alerts.hh /home/ccb63/Downloads/devtools/checkout/coot/lbg/solvent-exposure-difference.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/lbg'
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/lbg/lbg.glade /home/ccb63/Downloads/devtools/checkout/coot/lbg/lbg-callbacks.cc '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/lbg'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/lbg'
Making install in cootaneer
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/cootaneer'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/cootaneer'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcootaneer.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcootaneer.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcootaneer.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so.0 || { rm -f libcootaneer.so.0 && ln -s libcootaneer.so.0.0.0 libcootaneer.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so || { rm -f libcootaneer.so && ln -s libcootaneer.so.0.0.0 libcootaneer.so; }; })
libtool: install: /usr/bin/install -c .libs/libcootaneer.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcootaneer.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/cootaneer/cootaneer-llk-2.40.dat '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/cootaneer'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/cootaneer'
Making install in cootilus
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/cootilus'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/cootilus'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcootilus.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: /usr/bin/install -c .libs/libcootilus.so.0.0.0 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcootilus.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcootilus.so.0.0.0 libcootilus.so.0 || { rm -f libcootilus.so.0 && ln -s libcootilus.so.0.0.0 libcootilus.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcootilus.so.0.0.0 libcootilus.so || { rm -f libcootilus.so && ln -s libcootilus.so.0.0.0 libcootilus.so; }; })
libtool: install: /usr/bin/install -c .libs/libcootilus.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcootilus.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/cootilus/nautilus_lib.pdb '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/cootilus'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/cootilus'
Making install in goograph
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/goograph'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/goograph'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-goograph.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-goograph.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/goograph; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-goograph.la -rpath /opt/xtal/ccp4-7.0-linux64/lib goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -L/opt/xtal/ccp4-7.0-linux64/lib -lgoocanvas -pthread -L/opt/xtal/ccp4-7.0-linux64/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/goograph.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lsqlite3 -lcoot-utils -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lrt -lglib-2.0 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -pthread   -pthread -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-goograph.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-goograph.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so.0 || { rm -f libcoot-goograph.so.0 && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so || { rm -f libcoot-goograph.so && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-goograph.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-goograph.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/goograph'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/goograph'
Making install in pli
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pli'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pli'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot-pli.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot-pli.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/pli; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot-pli.la -rpath /opt/xtal/ccp4-7.0-linux64/lib protein-ligand-interactions.lo flev-annotations.lo pi-stacking.lo specs.lo ../lidia-core/libcoot-lidia-core.la -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lboost_python -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/protein-ligand-interactions.o .libs/flev-annotations.o .libs/pi-stacking.o .libs/specs.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -lsqlite3 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -Wl,-export-dynamic   -Wl,-soname -Wl,libcoot-pli.so.0 -o .libs/libcoot-pli.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot-pli.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-pli.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-pli.so.0.0.0 libcoot-pli.so.0 || { rm -f libcoot-pli.so.0 && ln -s libcoot-pli.so.0.0.0 libcoot-pli.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { ln -s -f libcoot-pli.so.0.0.0 libcoot-pli.so || { rm -f libcoot-pli.so && ln -s libcoot-pli.so.0.0.0 libcoot-pli.so; }; })
libtool: install: /usr/bin/install -c .libs/libcoot-pli.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-pli.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot/pli" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/pli"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pli/flev-annotations.hh /home/ccb63/Downloads/devtools/checkout/coot/pli/protein-ligand-interactions.hh /home/ccb63/Downloads/devtools/checkout/coot/pli/pi-stacking.hh /home/ccb63/Downloads/devtools/checkout/coot/pli/specs.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot/pli'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pli'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pli'
Making install in pyrogen
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
 /usr/bin/install -c pyrogen '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
test -z "/opt/xtal/ccp4-7.0-linux64/lib" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libcoot_py_restraints.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib'
libtool: install: warning: relinking `libcoot_py_restraints.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/pyrogen; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o libcoot_py_restraints.la -rpath /opt/xtal/ccp4-7.0-linux64/lib mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/mmff-restraints.o .libs/py-restraints.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -Wl,-export-dynamic   -Wl,-soname -Wl,libcoot_py_restraints.so.0 -o .libs/libcoot_py_restraints.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libcoot_py_restraints.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot_py_restraints.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { 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 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib && { 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: /usr/bin/install -c .libs/libcoot_py_restraints.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot_py_restraints.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib'
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   _pyrogen_swig.la pyrogen_boost.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages'
libtool: install: warning: relinking `_pyrogen_swig.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/pyrogen; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -module -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o _pyrogen_swig.la -rpath /opt/xtal/ccp4-7.0-linux64/lib/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 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lboost_python -L/opt/xtal/ccp4-7.0-linux64/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/opt/xtal/ccp4-7.0-linux64/lib -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/pyrogen-swig.o .libs/restraints.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coords/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot_py_restraints -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lsqlite3 -lpng -lcoot-analysis -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -Wl,-export-dynamic   -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0
libtool: install: /usr/bin/install -c .libs/_pyrogen_swig.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/_pyrogen_swig.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/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 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/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: /usr/bin/install -c .libs/_pyrogen_swig.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/_pyrogen_swig.la
libtool: install: warning: relinking `pyrogen_boost.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/pyrogen; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -module -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o pyrogen_boost.la -rpath /opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../pli/libcoot-pli.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lboost_python -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/restraints-boost.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coords/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot_py_restraints -lcoot-pli -lpthread -ldl -lutil -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coord-extras -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -lsqlite3 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lpython2.7 -lboost_python -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0
libtool: install: /usr/bin/install -c .libs/pyrogen_boost.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/pyrogen_boost.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/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 /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/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: /usr/bin/install -c .libs/pyrogen_boost.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/pyrogen_boost.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages'
make  install-exec-hook
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-hook'.
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pyrogen/pyrogen.py /home/ccb63/Downloads/devtools/checkout/coot/pyrogen/atom_types.py /home/ccb63/Downloads/devtools/checkout/coot/pyrogen/jay_util.py /home/ccb63/Downloads/devtools/checkout/coot/pyrogen/tautomer.py /home/ccb63/Downloads/devtools/checkout/coot/pyrogen/pyrogen_swig.py coot_git.py '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/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 `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pyrogen'
Making install in src
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/src'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/src'
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c coot-fix-nomenclature-errors '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
libtool: install: /usr/bin/install -c .libs/coot-fix-nomenclature-errors /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin/coot-fix-nomenclature-errors
test -z "/opt/xtal/ccp4-7.0-linux64/bin" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin"
 /usr/bin/install -c coot /home/ccb63/Downloads/devtools/checkout/coot/src/coot-density-score-by-residue /home/ccb63/Downloads/devtools/checkout/coot/src/dynarama '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/bin'
test -z "/opt/xtal/ccp4-7.0-linux64/libexec" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c coot-bin coot-density-score-by-residue-bin dynarama-bin '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec'
libtool: install: /usr/bin/install -c .libs/coot-bin /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/coot-bin
libtool: install: /usr/bin/install -c .libs/coot-density-score-by-residue-bin /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/coot-density-score-by-residue-bin
libtool: install: /usr/bin/install -c .libs/dynarama-bin /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/libexec/dynarama-bin
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   coot_embedded.la coot_extended.la '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages'
libtool: install: warning: relinking `coot_embedded.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/src; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -DPACKAGE_LOCALE_DIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot/locale\" -DPKGPYTHONDIR=\"/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot\" -DDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-centos-5-python-gtk2\" "-DCOOT_BUILD_INFO_STRING=\"CCP4, Oxfordshire\"" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/opt/xtal/ccp4-7.0-linux64/include -pthread -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYTHON -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -module --no-undefined -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o coot_embedded.la -rpath /opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages coot-embedded.lo ../lidia-core/libcoot-lidia-core.la -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lboost_python -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/coot-embedded.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -lsqlite3 -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -pthread -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1 -Wl,-export-dynamic   -pthread -Wl,-soname -Wl,coot_embedded.so.0 -o .libs/coot_embedded.so.0.0.0
libtool: install: /usr/bin/install -c .libs/coot_embedded.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot_embedded.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages && { ln -s -f coot_embedded.so.0.0.0 coot_embedded.so.0 || { rm -f coot_embedded.so.0 && ln -s coot_embedded.so.0.0.0 coot_embedded.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages && { ln -s -f coot_embedded.so.0.0.0 coot_embedded.so || { rm -f coot_embedded.so && ln -s coot_embedded.so.0.0.0 coot_embedded.so; }; })
libtool: install: /usr/bin/install -c .libs/coot_embedded.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot_embedded.la
libtool: install: warning: relinking `coot_extended.la'
libtool: install: (cd /home/ccb63/Downloads/devtools/builddir/coot/src; /bin/sh /home/ccb63/Downloads/devtools/builddir/coot/libtool  --tag CXX --mode=relink g++ -DPKGDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot\" -DPACKAGE_LOCALE_DIR=\"/opt/xtal/ccp4-7.0-linux64/share/coot/locale\" -DPKGPYTHONDIR=\"/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot\" -DDATADIR=\"/opt/xtal/ccp4-7.0-linux64/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-centos-5-python-gtk2\" "-DCOOT_BUILD_INFO_STRING=\"CCP4, Oxfordshire\"" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/opt/xtal/ccp4-7.0-linux64/include -pthread -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYTHON -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -I/opt/xtal/ccp4-7.0-linux64/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O3 -fno-strict-aliasing -pipe -mtune=core2 -fpermissive -Wall -Wno-unused -module --no-undefined -L/opt/xtal/ccp4-7.0-linux64/lib -s -Wl,--hash-style=both -Wl,--build-id=sha1 -o coot_extended.la -rpath /opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages coot-extended.lo ../pli/libcoot-pli.la -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7 -lboost_python -inst-prefix-dir /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot)
libtool: relink: g++ -shared -nostdlib /usr/lib/../lib64/crti.o /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtbeginS.o  .libs/coot-extended.o   -Wl,-rpath -Wl,/opt/xtal/ccp4-7.0-linux64/lib -L/home/ccb63/Downloads/devtools/builddir/coot/lidia-core/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/coot-utils/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/geometry/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/mini-mol/.libs -L/home/ccb63/Downloads/devtools/builddir/coot/utils/.libs -L/opt/xtal/ccp4-7.0-linux64/lib -L/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib -lcoot-pli -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -lsqlite3 -lpthread -ldl -lutil -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lpython2.7 -lboost_python -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/../../.. -lstdc++ -lm -lc -lgcc_s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/4.8.2/crtendS.o /usr/lib/../lib64/crtn.o  -pthread -mtune=core2 -Wl,--hash-style=both -Wl,--build-id=sha1   -pthread -Wl,-soname -Wl,coot_extended.so.0 -o .libs/coot_extended.so.0.0.0
libtool: install: /usr/bin/install -c .libs/coot_extended.so.0.0.0T /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot_extended.so.0.0.0
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages && { ln -s -f coot_extended.so.0.0.0 coot_extended.so.0 || { rm -f coot_extended.so.0 && ln -s coot_extended.so.0.0.0 coot_extended.so.0; }; })
libtool: install: (cd /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages && { ln -s -f coot_extended.so.0.0.0 coot_extended.so || { rm -f coot_extended.so && ln -s coot_extended.so.0.0.0 coot_extended.so; }; })
libtool: install: /usr/bin/install -c .libs/coot_extended.lai /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot_extended.la
libtool: install: warning: remember to run `libtool --finish /opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages'
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages"
 /usr/bin/install -c -m 644 coot.py /home/ccb63/Downloads/devtools/checkout/coot/src/coot.pth '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages'
Byte-compiling python modules...
coot.py
Byte-compiling python modules (optimized versions) ...
coot.py
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages"
 /usr/bin/install -c coot.py /home/ccb63/Downloads/devtools/checkout/coot/src/coot.pth '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages'
test -z "/opt/xtal/ccp4-7.0-linux64/include/coot/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/src/crunch-model.hh '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/include/coot/coot'
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/src/dynarama.glade '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/src'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/src'
Making install in data
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Making install in rama-coeffs
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/rama-coeffs'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/rama-coeffs'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/data/rama/zo-tables" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data/rama/zo-tables"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/data/rama-coeffs/all-non-pre-pro.tab /home/ccb63/Downloads/devtools/checkout/coot/data/rama-coeffs/coeffsolution.dat '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data/rama/zo-tables'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/rama-coeffs'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/rama-coeffs'
Making install in cho-models
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-models'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-models'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/data/cho-models" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data/cho-models"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-1-NAG-NAG-ASN-ASN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-BMA-BETA1-6-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-MAN-ALPHA1-3-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-2-FUC-BETA1-3-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-BMA-BETA1-6-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-MAN-ALPHA1-3-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-2-FUC-BETA1-6-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-MAN-ALPHA1-3-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-MAN-ALPHA1-6-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-2-FUL-ALPHA1-3-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-MAN-ALPHA1-4-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-MAN-ALPHA1-6-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-2-FUL-ALPHA1-6-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-MAN-ALPHA1-6-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-NAG-BETA1-2-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-2-NAG-BETA1-4-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-MAN-ALPHA1-6-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-6-GAL-BETA1-4-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-3-BMA-BETA1-3-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-NAG-BETA1-4-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-6-MAN-ALPHA1-2-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-3-BMA-BETA1-4-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-BMA-BETA1-2-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-7-GLC-ALPHA1-3-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-3-MAN-ALPHA1-4-NAG.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-BMA-BETA1-6-MAN.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-4-BMA-BETA1-3-BMA.tab /home/ccb63/Downloads/devtools/checkout/coot/data/cho-models/model-level-5-MAN-ALPHA1-2-MAN.tab '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data/cho-models'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-models'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-models'
Making install in cho-acedrg
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-acedrg'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-acedrg'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/data/cho-acedrg" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data/cho-acedrg"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/data/cho-acedrg/BMA-acedrg.cif /home/ccb63/Downloads/devtools/checkout/coot/data/cho-acedrg/FUC-acedrg.cif /home/ccb63/Downloads/devtools/checkout/coot/data/cho-acedrg/MAN-acedrg.cif /home/ccb63/Downloads/devtools/checkout/coot/data/cho-acedrg/NAG-acedrg.cif /home/ccb63/Downloads/devtools/checkout/coot/data/cho-acedrg/SIA-acedrg.cif /home/ccb63/Downloads/devtools/checkout/coot/data/cho-acedrg/XYP-acedrg.cif '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data/cho-acedrg'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-acedrg'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data/cho-acedrg'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/data" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/data/tutorial-modern.pdb /home/ccb63/Downloads/devtools/checkout/coot/data/rnasa-1.8-all_refmac1.mtz /home/ccb63/Downloads/devtools/checkout/coot/data/ligands.db '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/data'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/data'
Making install in man
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/man'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/man'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/man/man1" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1"
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-density-score-by-residue.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-density-score-by-residue.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-compare-dictionaries.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-compare-dictionaries.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-available-comp-id.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-available-comp-id.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-bfactan.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-bfactan.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-fix-nomenclature-errors.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-fix-nomenclature-errors.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-make-shelx-restraints.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-make-shelx-restraints.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/coot-mini-rsr.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/coot-mini-rsr.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/lidia.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/lidia.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/findwaters.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/findwaters.1'
 /usr/bin/install -c -m 644 '/home/ccb63/Downloads/devtools/checkout/coot/man/findligand.man' '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/man/man1/findligand.1'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/man'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/man'
Making install in rama-data
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/rama-data'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/rama-data'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/rama-data" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/rama-data"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-arg.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-asn.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-asp.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-cys.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-gln.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-glu.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-his.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-ile.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-leu.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-lys.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-met.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-phetyr.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-pro.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-ser.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-thr.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-trp.data /home/ccb63/Downloads/devtools/checkout/coot/rama-data/rota500-val.data '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/rama-data'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/rama-data'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/rama-data'
Making install in doc
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/doc'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/doc'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/doc'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/doc'
Making install in rcrane
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/rcrane'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/rcrane'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/rcrane/CHANGELOG.txt /home/ccb63/Downloads/devtools/checkout/coot/rcrane/buildPhosOxy.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/installRCrane.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/pseudoMolecule.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/selectMapDialog.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/LICENSE.txt /home/ccb63/Downloads/devtools/checkout/coot/rcrane/calcCoords.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/launch.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/pseudoPredictor.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/settings.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/chain.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/linearInterp.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/puckerList.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/smoothProb.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/NOTICE.txt /home/ccb63/Downloads/devtools/checkout/coot/rcrane/citationPopup.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/logo.svg /home/ccb63/Downloads/devtools/checkout/coot/rcrane/reviewSuitesGui.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/stats.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/README.txt /home/ccb63/Downloads/devtools/checkout/coot/rcrane/coot_gui_adapter.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/menu.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/revisionNum.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/strucCalc.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/__init__.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/coot_utils_adapter.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/nextPhos.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/rotData.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/suite.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/about.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/nucleotide.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/rotamerSeq.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/thetaEtaPredictor.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/bondLength.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/guiUtils.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/phenixRestraints.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/rotamerize.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/traceGui.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/buildInitSugar.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/icon.svg '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane'
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/rcrane/preLaunchCheck.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/safelog.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/extendChain.py /home/ccb63/Downloads/devtools/checkout/coot/rcrane/reportInputErrors.py '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane'
test -z "/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane/data" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane/data"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/bases.pdb /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/phosAngleSmoothed.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/sugarDists.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/c2p.pdb /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/phosDistSmoothed.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/sugarPhosSugarAngleSmoothed.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/c3p.pdb /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/pseudoChiSmoothed.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/thetaEtaClusts.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/dihedData.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/smoothedPuckerDist.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/endingPDists.csv /home/ccb63/Downloads/devtools/checkout/coot/rcrane/data/startingPDists.csv '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot/rcrane/data'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/rcrane'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/rcrane'
Making install in pixmaps
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Making install in icons
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps/icons'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps/icons'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
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 $icon | cut -d_ -f4`; \
        mkdir -p /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/icons/$THEME/$SIZE/$CONTEXT; \
        /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/icons/$icon /opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/icons/$THEME/$SIZE/$CONTEXT/$ICONFILE; \
    done;
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps/icons'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps/icons'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[4]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[4]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/coot-0.8.9.2.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/add-alt-conf.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/dna.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/probe-clash.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/add-alt-conf.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/edit-backbone.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/radacina_handcuffs-small.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/add-peptide-1.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/edit-chi.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/ramachandran.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/add-peptide-1.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/edit-chi.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/refine-1.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/add-water.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/emsley.jpg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/refine.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/anchor.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/env-distances.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/regularize-1.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/aniso-atom.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/env-distances.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/regularize.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/aniso-atom.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/eugene.jpg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/renumber-residues.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/appointment-new.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/flip-peptide.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/reset-view-32.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/atom-at-pointer.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/flip-peptide.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/reset-view-32.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/atom-at-pointer.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/generic-display-objects.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/reset-view.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/auto-fit-rotamer.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/geom.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/reset-view.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/auto-fit-rotamer.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/ghosts.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/residue-info.png '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps'
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/azerbaijan2.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/ghosts.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/residue-info.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/azerbaijan.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gln-asn-b-factors.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rigid-body.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/calculate-ghosts.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gln-asn-b-factorssvg.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rigid-body.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/cell+symm.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/glyco-structures.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rotamers.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/cell+symm.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gnome-run.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rotamers.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/change-chain-id.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/go-to-atom.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rtz.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rrz.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/chiral.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/go-to-ligand.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rtz.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rrz.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/chiral.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gtk-connect-16.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/scroll-wheel.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/connect-to-ccp4.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gtk-font.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/secondary-structure.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/connect-to-oca.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gtk-open-16.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/sequence-view.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/connect-to-usf.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gtk-open-24.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/sequence-view.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/connect-to-world.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/gtk-open.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/side-chain-180.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/kevin.jpg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/side-chain-180.svg '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps'
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/kevin-orig.jpg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/smiles.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/kleywegt.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/smiles.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/map.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/spin-view.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/coot-favicon.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/merge-molecules.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/spin-view.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/coot-icon.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/mutate-auto-fit.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/stereo-view.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/coot-save.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/mutate.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/stop.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/coot-save-symm.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/panel-screenshot.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/temperature.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/crosshairs.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/peptide-omega.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/temperature.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/crosshairs.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/peptide-omega.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/torsion-general.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/delete.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/phenixed.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/undo-1.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/delete.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/pink-pointer.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/undo-1.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/density-fit.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/pink-pointer.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/unknown-blob.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/diff-map.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/plane-distances.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/unknown-blob.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/diff-map.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/plane-distances.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/water-diff-map.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/display-manager.png '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps'
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/pointer-distances.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/water-drop.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/display-manager.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/pointer-distances.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/koppi-green-tick-64.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rygle-red-cross-64.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/forest51690-dwcheckno-incomplete-64.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/go-to-ligand.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/go-to-atom.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/azerbaijan.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/add-water.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/mutate.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/mutate-auto-fit.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/edit-backbone.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/torsion-general.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/anchor.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/regularize-1.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/refine-1.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/stock-zoom-follow-window-12.svg /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/stock-zoom-follow-window-12.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama_all.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama_gly.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama_pro.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama_non_gly_pro.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/curlew-long.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_all.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_gly.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_pro.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_non_gly_pro.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_ileval.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_pre_pro.png /home/ccb63/Downloads/devtools/checkout/coot/pixmaps/rama2_non_gly_pro_pre_pro_ileval.png '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot/pixmaps'
make[3]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot/pixmaps'
make[1]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Entering directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/opt/xtal/ccp4-7.0-linux64/share/appdata" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/appdata"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/coot.appdata.xml '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/appdata'
test -z "/opt/xtal/ccp4-7.0-linux64/share/applications" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/applications"
 /usr/bin/install -c -m 644 /home/ccb63/Downloads/devtools/checkout/coot/coot.desktop '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/applications'
test -z "/opt/xtal/ccp4-7.0-linux64/share/coot" || /bin/mkdir -p "/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot"
 /usr/bin/install -c -m 644 cootrc /home/ccb63/Downloads/devtools/checkout/coot/standard-residues.pdb /home/ccb63/Downloads/devtools/checkout/coot/colours.def /home/ccb63/Downloads/devtools/checkout/coot/mtrix-to-ncs-matrix.awk /home/ccb63/Downloads/devtools/checkout/coot/syminfo.lib '/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/share/coot'
make[2]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
make[1]: Leaving directory `/home/ccb63/Downloads/devtools/builddir/coot'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-map-utils.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-AngleInfo.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/_pyrogen_swig.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/pyrogen_boost.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot_embedded.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/python2.7/site-packages/coot_extended.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-isosurface.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-db-main.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-gtkgraph.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-pli.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-compat.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcootilus.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcootaneer.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-goograph.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-geometry.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-ideal.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coords.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-mini-mol.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-utils.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coord-extras.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libccp4mg-utils.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-tw.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-surface.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-electrostatics.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-coord-utils.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-cabuild.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot_py_restraints.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-lidia-core.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-analysis.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-protein-db.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-lidia.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-map-heavy.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-ligand.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-shelx.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-high-res.la'
Deleting .la file: u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot/opt/xtal/ccp4-7.0-linux64/lib/libcoot-skeleton.la'
Moving temporary DESTDIR u'/opt/xtal/ccp4-7.0-linux64/_jhbuild/root-coot' into build prefix
0 files remaining from previous build
Install complete: 919 files copied
Succeeded 2019-06-11 15:49:42.043