Login Name Tty Idle Login Time Office Office Phone Host emsley Paul Emsley tty1 4d Apr 24 19:45 (:0) emsley Paul Emsley pts/0 4d Apr 24 20:53 (:0) emsley Paul Emsley pts/3 3d Apr 26 13:08 (:0) emsley Paul Emsley pts/4 1d Apr 26 13:09 (:0) emsley Paul Emsley pts/5 1d Apr 26 13:11 (:0) emsley Paul Emsley pts/2 1d Apr 27 18:33 (:0) emsley Paul Emsley pts/6 45 Apr 29 14:58 (garib-pc-1.lmb.internal) emsley Paul Emsley pts/7 Apr 29 15:07 (garib-pc-1.lmb.internal) emsley Paul Emsley pts/8 8 Apr 29 15:56 (garib-pc-1.lmb.internal) From tar file: /d/emsley/autobuild/building/sources/coot-0.8.9.2-pre-revision-7428.tar.gz building in: /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre CFLAGS: CXXFLAGS: -g -O CPPFLAGS: LDFLAGS: PATH: /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc using this guile: /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/guile ./configure --prefix=/d/emsley/autobuild/install-33-pre-release-gtk3-python --with-fftw-prefix=/d/emsley/autobuild/install-33-pre-release-gtk3-python --with-goocanvas-prefix=/d/emsley/autobuild/install-33-pre-release-gtk3-python --with-glut-prefix=/d/emsley/autobuild/install-33-pre-release-gtk3-python COOT_BUILD_INFO_STRING=built by: Paul Emsley build-host: charybdis on: Sun 29 Apr 1710.58 BST 2018 --with-guile --with-python --with-pygobject --disable-shared configure: WARNING: unrecognized options: --with-pygobject checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking 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... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... 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... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/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 /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... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking 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... no checking whether to build static libraries... yes checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... 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... no checking for mmdb2... yes checking for ssm... yes no checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile... /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/guile checking for guile-config... /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/guile-config checking for guile-tools... /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/guile-tools checking libguile compile flags... -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -P -pthread checking libguile link flags... -P -pthread -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lguile -lltdl -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lgmp -lcrypt -lm -lltdl checking for Guile-Lib... yes checking GUILE_VERSION: 1.8 checking for gsl-config... /d/emsley/autobuild/install-33-pre-release-gtk3-python/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 python version... 3.6 checking for python platform... linux checking for python script directory... ${prefix}/lib/python3.6/site-packages checking for python extension module directory... ${exec_prefix}/lib/python3.6/site-packages checking for guile-gtk... checking for boostlib >= 1.20.0... configure: We could not detect the boost libraries (version 1.20 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in . See http://randspringer.de/boost for more documentation. checking for python3.6... /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/python3.6 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/python3.6m checking for Python library path... -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lpython3.6m checking for Python site-packages path... /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... File "", line 1 import distutils.sysconfig; import os; conf = distutils.sysconfig.get_config_var; print (conf('LINKFORSHARED') if os.name <> 'nt' else '') ^ SyntaxError: invalid syntax checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... no checking libglade... no checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... 7.32.0 checking build type... Linux-x86_64-scientific-linux-7.4-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: --with-pygobject Making all in auxil make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' Making all in catcheck make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/catcheck' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/catcheck' Making all in rama make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/rama' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/rama' Making all in sec-str make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/sec-str' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/strand-analysis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/strand-analysis' Making all in vectors make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/vectors' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/vectors' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' Making all in scheme make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/scheme' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/scheme' Making all in python make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python' Making all in pdb-templates make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pdb-templates' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pdb-templates' Making all in macros make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/macros' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/macros' Making all in compat make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/compat' /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O2 -Wall -Wunused -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O2 -Wall -Wunused -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c -o getopt1.lo getopt1.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O2 -Wall -Wunused -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O2 -Wall -Wunused -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o mv -f .deps/getopt.Tpo .deps/getopt.Plo mv -f .deps/getopt1.Tpo .deps/getopt1.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Wall -Wunused -o libcoot-compat.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib getopt.lo getopt1.lo libtool: link: ar cru .libs/libcoot-compat.a getopt.o getopt1.o libtool: link: ranlib .libs/libcoot-compat.a libtool: link: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/compat' Making all in utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c -o coot-utils.lo coot-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c -o coot-fasta.lo coot-fasta.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c -o atomic-numbers.lo atomic-numbers.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" 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-I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT dodec.lo -MD -MP -MF .deps/dodec.Tpo -c -o dodec.lo dodec.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT win-compat.lo -MD -MP -MF .deps/win-compat.Tpo -c -o 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win-compat.o mv -f .deps/win-compat.Tpo .deps/win-compat.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT align-utils.lo -MD -MP -MF .deps/align-utils.Tpo -c -o align-utils.lo align-utils.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 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-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT pir-alignment.lo -MD -MP -MF .deps/pir-alignment.Tpo -c -o pir-alignment.lo pir-alignment.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -g -O -Wall -Wno-unused -MT pir-alignment.lo -MD -MP -MF .deps/pir-alignment.Tpo -c pir-alignment.cc -o pir-alignment.o mv -f .deps/align-utils.Tpo .deps/align-utils.Plo mv -f .deps/coot-fasta.Tpo .deps/coot-fasta.Plo mv -f .deps/hsv-rgb.Tpo .deps/hsv-rgb.Plo mv -f .deps/atomic-numbers.Tpo .deps/atomic-numbers.Plo mv -f .deps/dodec.Tpo .deps/dodec.Plo mv -f .deps/pir-alignment.Tpo .deps/pir-alignment.Plo mv -f .deps/coot-utils.Tpo .deps/coot-utils.Plo mv -f .deps/gdk-keysyms.Tpo .deps/gdk-keysyms.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-utils.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib coot-utils.lo coot-fasta.lo atomic-numbers.lo gdk-keysyms.lo hsv-rgb.lo dodec.lo win-compat.lo threads.lo align-utils.lo pir-alignment.lo libtool: link: ar cru .libs/libcoot-utils.a coot-utils.o coot-fasta.o atomic-numbers.o gdk-keysyms.o hsv-rgb.o dodec.o win-compat.o threads.o align-utils.o pir-alignment.o libtool: link: ranlib .libs/libcoot-utils.a libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils' Making all in protein_db make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/protein_db' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT protein_db.lo -MD -MP -MF .deps/protein_db.Tpo -c -o protein_db.lo protein_db.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT protein_db_utils.lo -MD -MP -MF .deps/protein_db_utils.Tpo -c -o protein_db_utils.lo protein_db_utils.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT rna_db.lo -MD -MP -MF .deps/rna_db.Tpo -c -o rna_db.lo rna_db.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT protein_db.lo -MD -MP -MF .deps/protein_db.Tpo -c protein_db.cpp -o protein_db.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT protein_db_utils.lo -MD -MP -MF .deps/protein_db_utils.Tpo -c protein_db_utils.cpp -o protein_db_utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT rna_db.lo -MD -MP -MF .deps/rna_db.Tpo -c rna_db.cpp -o rna_db.o mv -f .deps/rna_db.Tpo .deps/rna_db.Plo mv -f .deps/protein_db_utils.Tpo .deps/protein_db_utils.Plo mv -f .deps/protein_db.Tpo .deps/protein_db.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-protein-db.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib protein_db.lo protein_db_utils.lo rna_db.lo -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lmmdb2 libtool: link: ar cru .libs/libcoot-protein-db.a protein_db.o protein_db_utils.o rna_db.o libtool: link: ranlib .libs/libcoot-protein-db.a libtool: link: ( cd ".libs" && rm -f "libcoot-protein-db.la" && ln -s "../libcoot-protein-db.la" "libcoot-protein-db.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/protein_db' Making all in mini-mol make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c -o mini-mol.lo mini-mol.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c -o mini-mol-utils.lo mini-mol-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c -o atom-quads.lo atom-quads.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -o mini-mol-utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -o mini-mol.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -o atom-quads.o mv -f .deps/mini-mol-utils.Tpo .deps/mini-mol-utils.Plo mv -f .deps/atom-quads.Tpo .deps/atom-quads.Plo mv -f .deps/mini-mol.Tpo .deps/mini-mol.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-mini-mol.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lmmdb2 -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 libtool: link: ar cru .libs/libcoot-mini-mol.a mini-mol.o mini-mol-utils.o atom-quads.o libtool: link: ranlib .libs/libcoot-mini-mol.a libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol' Making all in geometry make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/geometry' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE 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-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT available-comp-id.o -MD -MP -MF .deps/available-comp-id.Tpo -c -o available-comp-id.o available-comp-id.cc mv -f .deps/energy-lib.Tpo .deps/energy-lib.Plo mv -f .deps/available-comp-id.Tpo .deps/available-comp-id.Po mv -f .deps/chem_mods.Tpo .deps/chem_mods.Plo mv -f .deps/compare-dictionaries.Tpo .deps/compare-dictionaries.Po mv -f .deps/make-shelx-restraints.Tpo .deps/make-shelx-restraints.Po mv -f .deps/dict-utils.Tpo .deps/dict-utils.Plo mv -f .deps/cif-parse.Tpo .deps/cif-parse.Plo mv -f .deps/protein-geometry.Tpo .deps/protein-geometry.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-geometry.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/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/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lmmdb2 libtool: link: ar cru .libs/libcoot-geometry.a protein-geometry.o protein-geometry-mmdb.o read-sbase.o energy-lib.o chem_mods.o srs-interface.o protein-donor-acceptors.o lbg-graph.o dreiding.o dict-utils.o cif-parse.o main-chain.o residue-and-atom-specs.o mol-utils-2.o libtool: link: ranlib .libs/libcoot-geometry.a libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o ./libcoot-geometry.la /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -o coot-make-shelx-restraints make-shelx-restraints.o ./libcoot-geometry.la /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -o coot-available-comp-id available-comp-id.o ./libcoot-geometry.la libtool: link: g++ -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o ./.libs/libcoot-geometry.a -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -L=/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib:-L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib: /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol/.libs/libcoot-mini-mol.a /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-ccp4.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-cif.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-minimol.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-mmdb.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-cns.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-phs.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-contrib.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-core.so -lsrfftw -lsfftw -lpthread /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4c.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libmmdb2.so -Wl,-rpath -Wl,/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -Wl,-rpath -Wl,/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib libtool: link: g++ -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -g -O -Wall -Wno-unused -o coot-available-comp-id available-comp-id.o ./.libs/libcoot-geometry.a -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -L=/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib:-L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib: /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol/.libs/libcoot-mini-mol.a /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-ccp4.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-cif.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-minimol.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-mmdb.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-cns.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-phs.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-contrib.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-core.so -lsrfftw -lsfftw -lpthread /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4c.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libmmdb2.so -Wl,-rpath -Wl,/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -Wl,-rpath -Wl,/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib libtool: link: g++ -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -g -O -Wall -Wno-unused -o coot-make-shelx-restraints make-shelx-restraints.o ./.libs/libcoot-geometry.a -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -L=/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib:-L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib: /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol/.libs/libcoot-mini-mol.a /d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-ccp4.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-cif.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-minimol.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-mmdb.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-cns.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-phs.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-contrib.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libclipper-core.so -lsrfftw -lsfftw -lpthread /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4c.so /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libmmdb2.so -Wl,-rpath -Wl,/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -Wl,-rpath -Wl,/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/geometry' Making all in coot-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-utils' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" 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-DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-coord-utils-nucleotides.lo -MD -MP -MF .deps/coot-coord-utils-nucleotides.Tpo -c -o coot-coord-utils-nucleotides.lo coot-coord-utils-nucleotides.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT 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-DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-h-bonds.lo -MD -MP -MF .deps/coot-h-bonds.Tpo -c -o coot-h-bonds.lo coot-h-bonds.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DUSE_GUILE -DUSE_PYTHON 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-I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSphereTriangle.lo -MD -MP -MF .deps/CXXSphereTriangle.Tpo -c CXXSphereTriangle.cpp -o CXXSphereTriangle.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXCircleNode.lo -MD -MP -MF .deps/CXXCircleNode.Tpo -c CXXCircleNode.cpp -o CXXCircleNode.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXCoord.lo -MD -MP -MF .deps/CXXCoord.Tpo -c CXXCoord.cpp -o CXXCoord.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSphereTriangleEdge.lo -MD -MP -MF .deps/CXXSphereTriangleEdge.Tpo -c CXXSphereTriangleEdge.cpp -o CXXSphereTriangleEdge.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -o CXXChargeTable.o In file included from CXXNewHood.h:22:0, from CXXSphereElement.cpp:19: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ In file included from CXXNewHood.h:22:0, from CXXCircle.cpp:12: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ In file included from CXXNewHood.h:22:0, from CXXCircleNode.cpp:13: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ mv -f .deps/CXXCoord.Tpo .deps/CXXCoord.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c -o CXXSurface.lo CXXSurface.cpp mv -f .deps/CXXSphereNode.Tpo .deps/CXXSphereNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXCreator.lo -MD -MP -MF .deps/CXXCreator.Tpo -c -o CXXCreator.lo CXXCreator.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c CXXSurface.cpp -o CXXSurface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXCreator.lo -MD -MP -MF .deps/CXXCreator.Tpo -c CXXCreator.cpp -o CXXCreator.o In file included from CXXNewHood.h:22:0, from CXXSurface.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ CXXSurface.cpp:593:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(nSelAtoms, SelAtom, cout, unitSphereAtOrigin, vdwBallPntrs, contactMap, ContextSelAtom, splitReentrantProbes) schedule(dynamic, 100) //num_threads(2) ^ CXXSurface.cpp:597:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical(cout) ^ CXXSurface.cpp:618:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) ^ mv -f .deps/CXXSphereTriangleEdge.Tpo .deps/CXXSphereTriangleEdge.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSurfaceVertex.lo -MD -MP -MF .deps/CXXSurfaceVertex.Tpo -c -o CXXSurfaceVertex.lo CXXSurfaceVertex.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSurfaceVertex.lo -MD -MP -MF .deps/CXXSurfaceVertex.Tpo -c CXXSurfaceVertex.cpp -o CXXSurfaceVertex.o mv -f .deps/CXXSphereTriangle.Tpo .deps/CXXSphereTriangle.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXException.lo -MD -MP -MF .deps/CXXException.Tpo -c -o CXXException.lo CXXException.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXException.lo -MD -MP -MF .deps/CXXException.Tpo -c CXXException.cpp -o CXXException.o CXXSurface.cpp: In member function ‘int CXXSurface::calculateVDWFromAtoms(mmdb::PManager, int, int, double, double, bool)’: CXXSurface.cpp:497:45: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete vdwBallPntrs[i]; ^ CXXSurface.cpp:502:54: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete contextBallPntrs[i]; ^ CXXSurface.cpp: In member function ‘int CXXSurface::calculateAccessibleFromAtoms(mmdb::PManager, int, int, double, double, bool)’: CXXSurface.cpp:549:45: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete vdwBallPntrs[i]; ^ CXXSurface.cpp:554:54: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete contextBallPntrs[i]; ^ mv -f .deps/CXXException.Tpo .deps/CXXException.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c -o CXXTorusElement.lo CXXTorusElement.cpp CXXSurface.cpp: In member function ‘int CXXSurface::calculateFromAtoms(mmdb::PManager, int, int, double, double, bool)’: CXXSurface.cpp:634:79: warning: deleting object of polymorphic class type ‘CXXAtomBall’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete static_cast(vdwBallPntrs[i]); ^ CXXSurface.cpp:637:87: warning: deleting object of polymorphic class type ‘CXXAtomBall’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete static_cast(contextBallPntrs[i]); ^ CXXSurface.cpp:641:76: warning: deleting object of polymorphic class type ‘CXXReentrantProbeBall’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] delete static_cast(reentrantProbes[i]); ^ libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c CXXTorusElement.cpp -o CXXTorusElement.o In file included from CXXNewHood.h:22:0, from CXXTorusElement.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ mv -f .deps/CXXCircle.Tpo .deps/CXXCircle.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c -o CXXFFTSolventMap.lo CXXFFTSolventMap.cpp mv -f .deps/CXXSurfaceVertex.Tpo .deps/CXXSurfaceVertex.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c -o CXXTorusNode.lo CXXTorusNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c CXXFFTSolventMap.cpp -o CXXFFTSolventMap.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c CXXTorusNode.cpp -o CXXTorusNode.o mv -f .deps/CXXChargeTable.Tpo .deps/CXXChargeTable.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c -o CXXFortranFile.lo CXXFortranFile.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp -o CXXFortranFile.o mv -f .deps/CXXTorusNode.Tpo .deps/CXXTorusNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c -o CXXNewHood.lo CXXNewHood.cpp mv -f .deps/CXXCreator.Tpo .deps/CXXCreator.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c -o CXXTriangle.lo CXXTriangle.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c CXXNewHood.cpp -o CXXNewHood.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c CXXTriangle.cpp -o CXXTriangle.o In file included from CXXNewHood.h:22:0, from CXXNewHood.cpp:15: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ CXXNewHood.cpp:346:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (circleNodes) ^ CXXNewHood.cpp:377:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) ^ CXXNewHood.cpp:410:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) ^ mv -f .deps/CXXFortranFile.Tpo .deps/CXXFortranFile.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c -o CXXNode.lo CXXNode.cpp mv -f .deps/CXXFFTSolventMap.Tpo .deps/CXXFFTSolventMap.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c -o CXXQADSurface.lo CXXQADSurface.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c CXXQADSurface.cpp -o CXXQADSurface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c CXXNode.cpp -o CXXNode.o mv -f .deps/CXXNode.Tpo .deps/CXXNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXBall.lo -MD -MP -MF .deps/CXXBall.Tpo -c -o CXXBall.lo CXXBall.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXBall.lo -MD -MP -MF .deps/CXXBall.Tpo -c CXXBall.cpp -o CXXBall.o mv -f .deps/CXXTorusElement.Tpo .deps/CXXTorusElement.Plo In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurface.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -o CXXQADSurfaceStaticData.o In file included from CXXBall.cpp:10:0: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ CXXBall.cpp:34:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(delta, nBalls, contactMap, aSurface, raggedEdges, insideOrOutside, ballPntrs) schedule(dynamic, 10) //num_threads(2) ^ CXXBall.cpp:83:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(trimmedBalls, contactMap, insideOrOutside, reformattedEdges, delta, aSurface) schedule(dynamic, 10) //num_threads(2) ^ CXXBall.cpp:197:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared (binnedballs, ballRadiusX2, limits, binWidth, nBins, balls, contactMap) schedule(dynamic,10) //num_threads(2) ^ mv -f .deps/CXXTriangle.Tpo .deps/CXXTriangle.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c -o CXXSpace.lo CXXSpace.cpp In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurfaceStaticData.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -o CXXSpace.o mv -f .deps/CXXSphereElement.Tpo .deps/CXXSphereElement.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c -o CXXUtils.lo CXXUtils.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I../coot-utils -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c CXXUtils.cpp -o CXXUtils.o mv -f .deps/CXXCircleNode.Tpo .deps/CXXCircleNode.Plo mv -f .deps/CXXQADSurfaceStaticData.Tpo .deps/CXXQADSurfaceStaticData.Plo mv -f .deps/CXXNewHood.Tpo .deps/CXXNewHood.Plo mv -f .deps/CXXSpace.Tpo .deps/CXXSpace.Plo mv -f .deps/CXXSurface.Tpo .deps/CXXSurface.Plo mv -f .deps/CXXBall.Tpo .deps/CXXBall.Plo mv -f .deps/CXXUtils.Tpo .deps/CXXUtils.Plo mv -f .deps/CXXQADSurface.Tpo .deps/CXXQADSurface.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-electrostatics.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXBall.lo CXXQADSurfaceStaticData.lo CXXSpace.lo CXXUtils.lo -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lsrfftw -lsfftw -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lmmdb2 libtool: link: ar cru .libs/libcoot-electrostatics.a CXXSphereElement.o CXXChargeTable.o CXXSphereNode.o CXXCircle.o CXXSphereTriangle.o CXXCircleNode.o CXXSphereTriangleEdge.o CXXCoord.o CXXSurface.o CXXCreator.o CXXSurfaceVertex.o CXXException.o CXXTorusElement.o CXXFFTSolventMap.o CXXTorusNode.o CXXFortranFile.o CXXNewHood.o CXXTriangle.o CXXNode.o CXXQADSurface.o CXXBall.o CXXQADSurfaceStaticData.o CXXSpace.o CXXUtils.o libtool: link: ranlib .libs/libcoot-electrostatics.a libtool: link: ( cd ".libs" && rm -f "libcoot-electrostatics.la" && ln -s "../libcoot-electrostatics.la" "libcoot-electrostatics.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/surface' Making all in coot-surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-surface' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c -o coot-surface.lo coot-surface.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c -o rgbreps.lo rgbreps.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -o coot-surface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -o rgbreps.o mv -f .deps/rgbreps.Tpo .deps/rgbreps.Plo mv -f .deps/coot-surface.Tpo .deps/coot-surface.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-surface.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lmmdb2 -L/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lglut -L/usr/X11R6/lib64 -lGL libtool: link: ar cru .libs/libcoot-surface.a coot-surface.o rgbreps.o libtool: link: ranlib .libs/libcoot-surface.a libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-surface' Making all in lidia-core make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lidia-core' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT lbg-shared.lo -MD -MP -MF .deps/lbg-shared.Tpo -c -o lbg-shared.lo lbg-shared.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include 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-I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT chemical-feature-clusters.lo -MD -MP -MF .deps/chemical-feature-clusters.Tpo -c chemical-feature-clusters.cc -o chemical-feature-clusters.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT bond-table-record-t.lo -MD -MP -MF .deps/bond-table-record-t.Tpo -c bond-table-record-t.cc -o bond-table-record-t.o mv -f .deps/atom-types.Tpo .deps/atom-types.Plo mv -f .deps/chemical-feature-clusters.Tpo .deps/chemical-feature-clusters.Plo mv -f .deps/bond-table-record-t.Tpo .deps/bond-table-record-t.Plo mv -f .deps/lbg-shared.Tpo .deps/lbg-shared.Plo mv -f .deps/lig-build.Tpo .deps/lig-build.Plo mv -f .deps/lbg-molfile.Tpo .deps/lbg-molfile.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-lidia-core.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/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 libtool: link: ar cru .libs/libcoot-lidia-core.a lbg-shared.o lbg-molfile.o lig-build.o rdkit-interface.o cod-types.o bond-record-container-t.o cod-atom-type-t.o cod-atom-types.o bond-table-record-t.o chemical-feature-clusters.o atom-types.o libtool: link: ranlib .libs/libcoot-lidia-core.a libtool: link: ( cd ".libs" && rm -f "libcoot-lidia-core.la" && ln -s "../libcoot-lidia-core.la" "libcoot-lidia-core.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lidia-core' Making all in coords make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coords' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc -o Bond_lines.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT cos-sin.lo -MD -MP -MF .deps/cos-sin.Tpo -c cos-sin.cc -o cos-sin.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT Cartesian.lo -MD -MP -MF .deps/Cartesian.Tpo -c Cartesian.cc -o Cartesian.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.cc -o utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT Bond_lines_ext.lo -MD -MP -MF .deps/Bond_lines_ext.Tpo -c Bond_lines_ext.cc -o Bond_lines_ext.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT mmdb-extras.lo -MD -MP -MF .deps/mmdb-extras.Tpo -c mmdb-extras.cc -o mmdb-extras.o mv -f .deps/utils.Tpo .deps/utils.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -g -O -Wall -Wno-unused -MT coot-close.lo -MD -MP -MF .deps/coot-close.Tpo -c -o coot-close.lo coot-close.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT coot-close.lo -MD -MP -MF .deps/coot-close.Tpo -c coot-close.cc -o coot-close.o mv -f .deps/cos-sin.Tpo .deps/cos-sin.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -g -O -Wall -Wno-unused -MT phenix-geo.lo -MD -MP -MF .deps/phenix-geo.Tpo -c -o phenix-geo.lo phenix-geo.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT phenix-geo.lo -MD -MP -MF .deps/phenix-geo.Tpo -c phenix-geo.cc -o phenix-geo.o mv -f .deps/Cartesian.Tpo .deps/Cartesian.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -g -O -Wall -Wno-unused -MT phenix-geo-bonds.lo -MD -MP -MF .deps/phenix-geo-bonds.Tpo -c -o phenix-geo-bonds.lo phenix-geo-bonds.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share\" -g -O -Wall -Wno-unused -MT phenix-geo-bonds.lo -MD -MP -MF .deps/phenix-geo-bonds.Tpo -c phenix-geo-bonds.cc -o phenix-geo-bonds.o mv -f .deps/coot-close.Tpo .deps/coot-close.Plo mv -f .deps/Bond_lines_ext.Tpo .deps/Bond_lines_ext.Plo mv -f .deps/phenix-geo.Tpo .deps/phenix-geo.Plo mv -f .deps/mmdb-crystal.Tpo .deps/mmdb-crystal.Plo mv -f .deps/mmdb.Tpo .deps/mmdb.Plo mv -f .deps/phenix-geo-bonds.Tpo .deps/phenix-geo-bonds.Plo mv -f .deps/mmdb-extras.Tpo .deps/mmdb-extras.Plo mv -f .deps/Bond_lines.Tpo .deps/Bond_lines.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-33-pre-release-gtk3-python/share"' -g -O -Wall -Wno-unused -o libcoot-coords.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/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 ../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/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib -lmmdb2 libtool: link: ar cru .libs/libcoot-coords.a Bond_lines.o Cartesian.o cos-sin.o mmdb-extras.o utils.o mmdb.o mmdb-crystal.o Bond_lines_ext.o coot-close.o phenix-geo.o phenix-geo-bonds.o libtool: link: ranlib .libs/libcoot-coords.a libtool: link: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coords' Making all in angles make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/angles' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c -o libcoot_AngleInfo_la-AngleInfo.lo `test -f 'AngleInfo.cc' || echo './'`AngleInfo.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo `test -f 'AngleInfo-angle-torsions-autogen.cc' || echo './'`AngleInfo-angle-torsions-autogen.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo `test -f 'AngleInfo-theta_2-autogen.cc' || echo './'`AngleInfo-theta_2-autogen.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o mv -f .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Plo mv -f .deps/libcoot_AngleInfo_la-AngleInfo.Tpo .deps/libcoot_AngleInfo_la-AngleInfo.Plo mv -f .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O1 -g -O -Wall -Wno-unused -o libcoot-AngleInfo.la -rpath /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo libtool: link: ar cru .libs/libcoot-AngleInfo.a libcoot_AngleInfo_la-AngleInfo.o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o libtool: link: ranlib .libs/libcoot-AngleInfo.a libtool: link: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/angles' Making all in skeleton make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/skeleton' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c -o graphical_skel.lo graphical_skel.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE 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-MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -o BuildCas.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -o dm-utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I.. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -o graphical_skel.o mv -f .deps/dm-utils.Tpo .deps/dm-utils.Plo mv -f .deps/graphical_skel.Tpo .deps/graphical_skel.Plo mv -f .deps/BuildCas.Tpo .deps/BuildCas.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-skeleton.la -rpath 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-DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c -o mgtree.lo mgtree.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c -o quat.lo quat.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.2-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c -o ppmutil.lo ppmutil.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -o geomutil.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -o ppmutil.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -o quat.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -o mgtree.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.2-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.2-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.2-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_PYTHON=\"3.6\" -I. -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-33-pre-release-gtk3-python/include -g -O -Wall -Wno-unused -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o mv -f .deps/quat.Tpo .deps/quat.Plo mv -f .deps/geomutil.Tpo .deps/geomutil.Plo mv -f .deps/cartesian.Tpo .deps/cartesian.Plo ppmutil.cc: In member function ‘void image_info::readpng(const char*)’: ppmutil.cc:2508:79: warning: ‘palette’ may be used uninitialized in this function [-Wmaybe-uninitialized] pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; ^ ppmutil.cc:2512:9: warning: ‘num_trans’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(row_pointers[i][j] cootrc make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre' 1 --------------------------------------------------------------- make install 1 ---------------------------------------------------------------- Making install in auxil make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' Making install in catcheck make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/catcheck' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/catcheck' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/catcheck' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/catcheck' Making install in rama make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/rama' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/rama' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/rama' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/rama' Making install in sec-str make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/sec-str' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/sec-str' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/sec-str' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/sec-str' Making install in strand-analysis make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/strand-analysis' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/strand-analysis' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/strand-analysis' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/strand-analysis' Making install in vectors make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/vectors' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/vectors' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/vectors' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil/vectors' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/auxil' Making install in scheme make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/scheme' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/scheme' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/scheme" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/scheme" /usr/bin/install -c -m 644 0-auto-rot.scm coot-utils.scm get-ebi.scm mutate.scm background-demo.scm demo-script.scm gtkin.scm my-readline.scm bit.scm extra-top-level.scm hello.scm raster3d.scm brute-lsqman.scm file-utils.scm junk.scm refmac.scm coot-gui.scm filter.scm libcheck.scm simple.scm coot.scm get-ebi.save.scm local-code.scm trivial.scm gap.scm remote-control.scm povray.scm coot-lsq.scm shelx.scm group-settings.scm fitting.scm americanisms.scm tips.scm tips-gui.scm generic-objects.scm cns2coot.scm extensions.scm ncs.scm create-server.scsh coot-crash-catcher.scm '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/scheme' /usr/bin/install -c -m 644 snarf-coot-docs.scm clear-backup.scm bones-reader.scm matrices.scm fascinating-things.scm shelx-extensions.scm parse-pisa-xml.scm check-for-updates.scm 3d-generator-import.scm gui-hole.scm gui-prosmart.scm get-recent-pdbe.scm json-reader.scm jligand.scm jligand-gui.scm redefine-functions.scm user-define-restraints.scm template-key-bindings.scm gui-add-linked-cho.scm ligand-check.scm run-mogul.scm contact-score-isolated-ligand.scm enhanced-ligand.scm gui-ligand-sliders.scm dictionary-generators.scm cho-restraints-from-models.scm interactive-nudge-residues.scm acedrg-link.scm '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/scheme' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/scheme' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/scheme' Making install in python make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot" /usr/bin/install -c -m 644 coot_utils.py get_ebi.py mutate.py background_demo.py hello.py raster3d.py brute_lsqman.py refmac.py coot_gui.py filter.py libcheck.py coot_load_modules.py local_code.py gap.py remote_control.py povray.py coot_lsq.py shelx.py group_settings.py fitting.py americanisms.py tips.py tips_gui.py generic_objects.py cns2coot.py extensions.py ncs.py create_server.py python_coot_docs.py clear_backup.py bones_reader.py shelx_extensions.py parse_pisa_xml.py check_for_updates.py 3d_generator_import.py gui_hole.py gui_prosmart.py get_recent_pdbe.py jligand.py jligand_gui.py '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot' /usr/bin/install -c -m 644 redefine_functions.py user_define_restraints.py template_key_bindings.py gui_add_linked_cho.py ligand_check.py run_mogul.py contact_score_isolated_ligand.py gui_contact_score_isolated_ligand.py enhanced_ligand.py gui_ligand_sliders.py dictionary_generators.py cho_restraints_from_models.py interactive_nudge_residues.py acedrg_link.py coot_toolbuttons.py rcrane_loader.py pdbe_validation_data.py ligand_validation_sliders.py chemical_feature_clusters.py res_spec_utils.py '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/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.pySorry: TabError: inconsistent use of tabs and spaces in indentation (coot_utils.py, line 349) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/get_ebi.py", line 70 print "BL WARNING:: retrieve of url %s failed" %url ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL WARNING:: retrieve of url %s failed" %url)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/mutate.py", line 26 print "sequence mismatch: molecule", chain_n_residues(chain_id, imol), "new sequences:", len(sequence) ^ SyntaxError: invalid syntax Sorry: TabError: inconsistent use of tabs and spaces in indentation (background_demo.py, line 37) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/hello.py", line 73 print hello_str ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(hello_str)? Sorry: TabError: inconsistent use of tabs and spaces in indentation (raster3d.py, line 41) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/brute_lsqman.py", line 52 print "lsqman failed - sorry. I don't know what to say." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("lsqman failed - sorry. I don't know what to say.")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/refmac.py", line 107 print "BL ERROR:: We cannot allocate $CCP4I_TCLTK so no wish available" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL ERROR:: We cannot allocate $CCP4I_TCLTK so no wish available")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/coot_gui.py", line 36 print "WARNING:: no gobject available" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("WARNING:: no gobject available")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/filter.py", line 27 print i, ls[i] ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(i, ls[i])? Sorry: TabError: inconsistent use of tabs and spaces in indentation (libcheck.py, line 65) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/coot_load_modules.py", line 130 print """BL WARNING:: could not import coot_python module!! Some things, esp. extensions, may be crippled!""" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("""BL WARNING:: could not import coot_python module!! Some things, esp. extensions, may be crippled!""")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/gap.py", line 138 close_ls = map(lambda (x, y): "close_molecule(" + str(x) + ")", fragment_list) ^ SyntaxError: invalid syntax File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/remote_control.py", line 41 print "in open_coot_listener_socket port: %s host %s" %(port_number, host_adress) ^ SyntaxError: invalid syntax File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/povray.py", line 57 print "calling povray with args: ", povray_args() ^ SyntaxError: invalid syntax Sorry: TabError: inconsistent use of tabs and spaces in indentation (coot_lsq.py, line 56) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/shelx.py", line 64 print "BL ERROR:: Cannot read ", fcf_filename ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL ERROR:: Cannot read ", fcf_filename)? Sorry: TabError: inconsistent use of tabs and spaces in indentation (fitting.py, line 43) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/generic_objects.py", line 66 print "BL WARNING:: no pygtk2. Function wont work!!!" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL WARNING:: no pygtk2. Function wont work!!!")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/cns2coot.py", line 40 print "BL WARNING:: Cannot read ", pdb_file ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL WARNING:: Cannot read ", pdb_file)? Sorry: TabError: inconsistent use of tabs and spaces in indentation (extensions.py, line 232) Sorry: TabError: inconsistent use of tabs and spaces in indentation (ncs.py, line 48) File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/create_server.py", line 22 print "BL DEBUG:: host, port", hostname,port ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL DEBUG:: host, port", hostname,port)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/python_coot_docs.py", line 21 print "to be done?" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("to be done?")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/clear_backup.py", line 83 print "Deleting old file %s from %s" %(file_name, dir_name) ^ SyntaxError: invalid syntax File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/bones_reader.py", line 74 print "found atom_colour." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("found atom_colour.")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/shelx_extensions.py", line 133 print "INFO:: problems reading file", ins_tmp_file ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("INFO:: problems reading file", ins_tmp_file)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/parse_pisa_xml.py", line 46 print "opened", file_name ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("opened", file_name)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/check_for_updates.py", line 137 print "run_download_binary_curl failed" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("run_download_binary_curl failed")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/3d_generator_import.py", line 56 print "BL WARNING:: Problem: home is", home # FIXME ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL WARNING:: Problem: home is", home # FIXME)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/gui_hole.py", line 48 print "Start pos set to:", start_pos ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Start pos set to:", start_pos)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/get_recent_pdbe.py", line 35 print " ".join(map(str, txt)) ^ SyntaxError: invalid syntax jligand.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.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/jligand.py", line 137 print " WARNING:: bond_length_from_atoms: atom_1 not a list:", atom_1 ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(" WARNING:: bond_length_from_atoms: atom_1 not a list:", atom_1)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/jligand_gui.py", line 30 print "BL INFO:: no java found" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL INFO:: no java found")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/user_define_restraints.py", line 16 print "BL DEBUG:: imol: %s spec 1: %s and 2: %s" %(imol, atom_spec_1, atom_spec_2) ^ SyntaxError: invalid syntax File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/template_key_bindings.py", line 20 print "No active atom" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("No active atom")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/gui_add_linked_cho.py", line 13 print "failed to get %s restraints" %comp_id ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("failed to get %s restraints" %comp_id)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/ligand_check.py", line 34 print "BL ERROR:: failed liagnd atoms not a number." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL ERROR:: failed liagnd atoms not a number.")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/contact_score_isolated_ligand.py", line 81 print generic_object_name(i), "is not in", coot_probe_object_names ^ SyntaxError: invalid syntax File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/enhanced_ligand.py", line 115 lambda (ref_comp_id_txt, new_comp_id_txt, new_cif_file_name_txt): match_this_residue_and_dictionary(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, new_cif_file_name_txt, ref_comp_id_txt, new_comp_id_txt)) ^ SyntaxError: invalid syntax File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/gui_ligand_sliders.py", line 14 print "Failed to read columms from file %s for map molecule %s" \ ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Failed to read columms from file %s for map molecule %s" \)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/cho_restraints_from_models.py", line 31 print "BL DEBUG:: --------------------- add_cho_restraints_for_residue: glyco_tree_residue_id:", id ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("BL DEBUG:: --------------------- add_cho_restraints_for_residue: glyco_tree_residue_id:", id)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/interactive_nudge_residues.py", line 11 print "imol:", imol ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("imol:", imol)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/acedrg_link.py", line 11 print "setting menu active ", default_option_value, count ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("setting menu active ", default_option_value, count)? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/coot_toolbuttons.py", line 63 print """BL ERROR:: coot_python module not available!! So we cannot make toolbar_separator!""" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("""BL ERROR:: coot_python module not available!! So we cannot make toolbar_separator!""")? File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane_loader.py", line 49 print "Cannot move ~/.coot-preferences/rcrane.py to ~/.coot-preferences/rcrane.py.bak" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Cannot move ~/.coot-preferences/rcrane.py to ~/.coot-preferences/rcrane.py.bak")? Sorry: TabError: inconsistent use of tabs and spaces in indentation (pdbe_validation_data.py, line 30) Sorry: TabError: inconsistent use of tabs and spaces in indentation (ligand_validation_sliders.py, line 37) Sorry: TabError: inconsistent use of tabs and spaces in indentation (chemical_feature_clusters.py, line 147) 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.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python' Making install in pdb-templates make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pdb-templates' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pdb-templates' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" /usr/bin/install -c -m 644 ASN-NAG-via-NAG-ASN.pdb pyranose-pyranose-via-BETA1-4.pdb pyranose-pyranose-via-ALPHA1-2.pdb pyranose-pyranose-via-ALPHA1-3.pdb pyranose-pyranose-via-ALPHA1-6.pdb SIA-pyranose-via-ALPHA2-3.pdb link-by-torsion-to-pyranose-core-ALPHA1-2.tab link-by-torsion-to-pyranose-core-ALPHA1-3.tab link-by-torsion-to-FUC-core-ALPHA1-3.tab link-by-torsion-to-FUC-core-ALPHA1-2.tab link-by-torsion-to-FUC-core-ALPHA1-6.tab link-by-torsion-to-pyranose-core-ALPHA1-6.tab link-by-torsion-to-pyranose-core-ALPHA2-3.tab link-by-torsion-to-pyranose-core-BETA1-2.tab link-by-torsion-to-pyranose-core-BETA1-3.tab link-by-torsion-to-pyranose-core-BETA1-4.tab link-by-torsion-to-pyranose-core-BETA1-6.tab link-by-torsion-to-pyranose-core-NAG-ASN.tab link-by-torsion-to-pyranose-core-XYP-BMA.tab NAG-decorations.tab BMA-decorations.tab MAN-decorations.tab GLC-decorations.tab GAL-decorations.tab FUC-decorations.tab FUL-decorations.tab XYP-decorations.tab theor-helix-70.pdb '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pdb-templates' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pdb-templates' Making install in macros make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/macros' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/macros' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/macros' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/macros' Making install in compat make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/compat' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/compat' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/compat" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/compat" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-compat.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 coot-getopt.h '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/compat' libtool: install: /usr/bin/install -c .libs/libcoot-compat.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-compat.la libtool: install: /usr/bin/install -c .libs/libcoot-compat.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-compat.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-compat.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-compat.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/compat' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/compat' Making install in utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/utils" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/utils" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-utils.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 coot-utils.hh coot-fasta.hh dodec.hh win-compat.hh ctpl_stl.h pir-alignment.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/utils' libtool: install: /usr/bin/install -c .libs/libcoot-utils.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-utils.la libtool: install: /usr/bin/install -c .libs/libcoot-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-utils.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-utils.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-utils.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/utils' Making install in protein_db make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/protein_db' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/protein_db' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/protein_db" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/protein_db" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/protein_db" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/protein_db" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-protein-db.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 protein.db '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/protein_db' /usr/bin/install -c -m 644 protein_db.h protein_db_utils.h rna_db.h '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/protein_db' libtool: install: /usr/bin/install -c .libs/libcoot-protein-db.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-protein-db.la libtool: install: /usr/bin/install -c .libs/libcoot-protein-db.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-protein-db.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-protein-db.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-protein-db.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/protein_db' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/protein_db' Making install in mini-mol make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/mini-mol" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/mini-mol" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-mini-mol.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 mini-mol.hh mini-mol-utils.hh atom-quads.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/mini-mol' libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-mini-mol.la libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-mini-mol.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-mini-mol.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-mini-mol.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/mini-mol' Making install in geometry make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/geometry' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/geometry' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/geometry" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/geometry" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-geometry.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interface.hh dict-utils.hh dict-mismatches.hh energy-lib.hh match-results.hh hb-types.hh main-chain.hh residue-and-atom-specs.hh chem_mods.hh mol-utils-2.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/geometry' libtool: install: /usr/bin/install -c .libs/libcoot-geometry.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-geometry.la libtool: install: /usr/bin/install -c .libs/libcoot-geometry.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-geometry.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-geometry.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-geometry.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c coot-compare-dictionaries coot-make-shelx-restraints coot-available-comp-id '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' libtool: install: /usr/bin/install -c coot-compare-dictionaries /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/coot-compare-dictionaries libtool: install: /usr/bin/install -c coot-make-shelx-restraints /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/coot-make-shelx-restraints libtool: install: /usr/bin/install -c coot-available-comp-id /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/coot-available-comp-id make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/geometry' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/geometry' Making install in coot-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-utils' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-utils' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/coot-utils" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/coot-utils" /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 '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 peak-search.hh coot-trim.hh coot-coord-utils.hh coot-map-utils.hh coot-coord-extras.hh coot-map-heavy.hh coot-lsq-types.h coot-shelx.hh coot-rama.hh xmap-stats.hh coot-h-bonds.hh lsq-improve.hh coot-hole.hh read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh emma.hh glyco-torsions.hh coot-least-squares.hh coot-density-stats.hh atom-overlaps.hh reduce.hh secondary-structure-headers.hh plane-utils.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/coot-utils' libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-utils.la libtool: install: /usr/bin/install -c .libs/libcoot-shelx.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-shelx.la libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-extras.la libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-utils.la libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-heavy.la libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-utils.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-utils.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-utils.a libtool: install: /usr/bin/install -c .libs/libcoot-shelx.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-shelx.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-shelx.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-shelx.a libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-extras.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-extras.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coord-extras.a libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-utils.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-utils.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-utils.a libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-heavy.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-heavy.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-map-heavy.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-utils' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-utils' Making install in surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/surface' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/surface' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" make[2]: Nothing to be done for `install-data-am'. /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-electrostatics.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-electrostatics.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-electrostatics.la libtool: install: /usr/bin/install -c .libs/libcoot-electrostatics.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-electrostatics.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-electrostatics.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-electrostatics.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/surface' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/surface' Making install in coot-surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-surface' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-surface' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" make[2]: Nothing to be done for `install-data-am'. /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-surface.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-surface.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-surface.la libtool: install: /usr/bin/install -c .libs/libcoot-surface.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-surface.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-surface.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-surface.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-surface' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coot-surface' Making install in lidia-core make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lidia-core' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lidia-core' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/lidia-core" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/lidia-core" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-lidia-core.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 lbg-shared.hh lbg-molfile.hh lig-build.hh rdkit-interface.hh use-rdkit.hh cod-types.hh neighbour-sorter.hh bond-record-container-t.hh bond-table-record-t.hh cod-atom-types.hh cod-atom-type-t.hh primes.hh chemical-feature-clusters.hh third-neighbour-info-t.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/lidia-core' libtool: install: /usr/bin/install -c .libs/libcoot-lidia-core.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia-core.la libtool: install: /usr/bin/install -c .libs/libcoot-lidia-core.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia-core.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia-core.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia-core.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lidia-core' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lidia-core' Making install in coords make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coords' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coords' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/coords" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/coords" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-coords.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 Bond_lines.h Cartesian.h cos-sin.h mmdb.h mmdb-extras.h utils.h mmdb-crystal.h Bond_lines_ext.h coot-close.hh phenix-geo.hh ramachandran-container.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/coords' libtool: install: /usr/bin/install -c .libs/libcoot-coords.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coords.la libtool: install: /usr/bin/install -c .libs/libcoot-coords.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coords.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coords.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-coords.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coords' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/coords' Making install in angles make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/angles' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/angles' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/angles" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/angles" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-AngleInfo.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 AngleInfo.h ncube.h wrapped-ncube.h '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/angles' libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-AngleInfo.la libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-AngleInfo.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-AngleInfo.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-AngleInfo.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/angles' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/angles' Making install in skeleton make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/skeleton' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/skeleton' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/skeleton" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/skeleton" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-skeleton.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 graphical_skel.h dm-utils.h BuildCas.h '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/skeleton' libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-skeleton.la libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-skeleton.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-skeleton.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-skeleton.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/skeleton' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/skeleton' Making install in ccp4mg-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ccp4mg-utils' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ccp4mg-utils' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ccp4mg-utils" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ccp4mg-utils" /bin/sh ../libtool --mode=install /usr/bin/install -c libccp4mg-utils.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 geomutil.h mgtree.h cartesian.h matrix.h quat.h ppmutil.h '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ccp4mg-utils' libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4mg-utils.la libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4mg-utils.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4mg-utils.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libccp4mg-utils.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ccp4mg-utils' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ccp4mg-utils' Making install in density-contour make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/density-contour' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/density-contour' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/density-contour" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/density-contour" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-isosurface.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 Vectors.h CIsoSurface.h density-contour-triangles.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/density-contour' libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-isosurface.la libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-isosurface.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-isosurface.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-isosurface.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/density-contour' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/density-contour' Making install in db-main make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/db-main' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/db-main' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/db-main" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/db-main" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-db-main.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 db-main.hh db-strands.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/db-main' libtool: install: /usr/bin/install -c .libs/libcoot-db-main.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-db-main.la libtool: install: /usr/bin/install -c .libs/libcoot-db-main.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-db-main.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-db-main.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-db-main.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/db-main' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/db-main' Making install in analysis make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/analysis' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/analysis' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/analysis" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/analysis" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-analysis.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 bfkurt.hh mogul-interface.hh stats.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/analysis' libtool: install: /usr/bin/install -c .libs/libcoot-analysis.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-analysis.la libtool: install: /usr/bin/install -c .libs/libcoot-analysis.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-analysis.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-analysis.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-analysis.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c coot-bfactan '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' libtool: install: /usr/bin/install -c coot-bfactan /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/coot-bfactan make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/analysis' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/analysis' Making install in ideal make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ideal' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ideal' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ideal" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ideal" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-ideal.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 test-indexing.hh simple-restraint.hh pepflip.hh regularize-minimol.hh lograma.h parallel-planes.hh torsion-bonds.hh extra-restraints.hh model-bond-deltas.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ideal' /bin/sh ../libtool --mode=install /usr/bin/install -c mini-rsr-bin '/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec' /usr/bin/install -c coot-mini-rsr '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' libtool: install: /usr/bin/install -c mini-rsr-bin /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/mini-rsr-bin libtool: install: /usr/bin/install -c .libs/libcoot-ideal.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ideal.la libtool: install: /usr/bin/install -c .libs/libcoot-ideal.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ideal.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ideal.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ideal.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ideal' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ideal' Making install in ligand make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ligand' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ligand' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ligand" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ligand" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-ligand.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 ligands-2016.db '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data' /usr/bin/install -c findwaters findligand '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' /usr/bin/install -c -m 644 ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh rigid-body.hh ideal-rna.hh rotamer.hh richardson-rotamer.hh torsion-general.hh primitive-chi-angles.hh dipole.hh base-pairing.hh backrub-rotamer.hh trace.hh multi-peptide.hh ligands-db.hh scored-coord.hh ligand-score-card.hh scored-molecule.hh map-point-cluster.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/ligand' /bin/sh ../libtool --mode=install /usr/bin/install -c findligand-bin findwaters-bin coot-make-ligands-db '/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec' libtool: install: /usr/bin/install -c .libs/libcoot-ligand.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ligand.la libtool: install: /usr/bin/install -c .libs/libcoot-ligand.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ligand.a libtool: install: /usr/bin/install -c findligand-bin /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/findligand-bin libtool: install: /usr/bin/install -c findwaters-bin /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/findwaters-bin libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ligand.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-ligand.a libtool: install: /usr/bin/install -c coot-make-ligands-db /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/coot-make-ligands-db libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ligand' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/ligand' Making install in high-res make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/high-res' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/high-res' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/high-res" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/high-res" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-high-res.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 high-res.hh coot-atom-graph.hh coot-node-info.hh sequence-assignment.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/high-res' libtool: install: /usr/bin/install -c .libs/libcoot-high-res.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-high-res.la libtool: install: /usr/bin/install -c .libs/libcoot-high-res.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-high-res.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-high-res.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-high-res.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/high-res' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/high-res' Making install in build make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/build' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/build' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/build" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/build" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-cabuild.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 CalphaBuild.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/build' libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-cabuild.la libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-cabuild.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-cabuild.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-cabuild.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/build' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/build' Making install in greg-tests make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/greg-tests' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/greg-tests' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/greg-tests' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/greg-tests' Making install in python-tests make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python-tests' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python-tests' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python-tests' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/python-tests' Making install in tw make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/tw' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/tw' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/tw" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/tw" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-tw.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 coot-tw.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/tw' libtool: install: /usr/bin/install -c .libs/libcoot-tw.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-tw.la libtool: install: /usr/bin/install -c .libs/libcoot-tw.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-tw.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-tw.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-tw.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/tw' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/tw' Making install in libgtkgraph make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/libgtkgraph' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/libgtkgraph' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" make[2]: Nothing to be done for `install-data-am'. /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-gtkgraph.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-gtkgraph.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-gtkgraph.la libtool: install: /usr/bin/install -c .libs/libcoot-gtkgraph.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-gtkgraph.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-gtkgraph.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-gtkgraph.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/libgtkgraph' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/libgtkgraph' Making install in lbg make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lbg' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lbg' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/lidia" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/lidia" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/lbg" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/lbg" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-lidia.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 lbg.hh w-atom.hh w-bond.hh wmolecule.hh topological-equivalence.hh graphics-c-interface-functions.hh lbg-drag-and-drop.hh qed-interface.hh alerts.hh solvent-exposure-difference.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/lbg' /usr/bin/install -c -m 644 3-c-new.svg 6-c-shadow-experiment.svg single.svg 3-c-other.svg 6-c.svg sp3.svg 3-c.svg 7-c.svg stereo-out.svg 4-c.svg 8-c.svg TheStructorr_magnifying_glass-32.svg 5-c.svg Anonymous_Architetto_--_Chiave.svg TheStructorr_magnifying_glass.svg 6-c-arom.svg charge.svg triple.svg 6-c-exp-2.svg double.svg Trash-hydrogens-Andy_Trash_Can.svg face-smile.svg 05_Hotel_Icon_Hair_Salon.svg '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps' /usr/bin/install -c -m 644 lbg.glade lbg-callbacks.cc '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot' /usr/bin/install -c -m 644 __init__.py fetch.py '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/lidia' libtool: install: /usr/bin/install -c .libs/libcoot-lidia.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia.la libtool: install: /usr/bin/install -c .libs/libcoot-lidia.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-lidia.a Byte-compiling python modules... __init__.pyfetch.py File "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/lidia/fetch.py", line 57 print "oops - found #REDIRECT but was redirected already!" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("oops - found #REDIRECT but was redirected already!")? Byte-compiling python modules (optimized versions) ... __init__.pyfetch.py libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c lidia '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' libtool: install: /usr/bin/install -c lidia /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/lidia make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lbg' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/lbg' Making install in cootaneer make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootaneer' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootaneer' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" /bin/sh ../libtool --mode=install /usr/bin/install -c libcootaneer.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 cootaneer-llk-2.40.dat '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot' libtool: install: /usr/bin/install -c .libs/libcootaneer.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootaneer.la libtool: install: /usr/bin/install -c .libs/libcootaneer.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootaneer.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootaneer.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootaneer.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootaneer' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootaneer' Making install in cootilus make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootilus' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootilus' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" /bin/sh ../libtool --mode=install /usr/bin/install -c libcootilus.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 nautilus_lib.pdb '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot' libtool: install: /usr/bin/install -c .libs/libcootilus.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootilus.la libtool: install: /usr/bin/install -c .libs/libcootilus.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootilus.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootilus.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcootilus.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootilus' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/cootilus' Making install in goograph make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/goograph' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/goograph' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" make[2]: Nothing to be done for `install-data-am'. /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-goograph.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-goograph.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-goograph.la libtool: install: /usr/bin/install -c .libs/libcoot-goograph.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-goograph.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-goograph.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-goograph.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/goograph' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/goograph' Making install in pli make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pli' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pli' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/pli" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/pli" /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-pli.la '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib' /usr/bin/install -c -m 644 flev-annotations.hh protein-ligand-interactions.hh pi-stacking.hh specs.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot/pli' libtool: install: /usr/bin/install -c .libs/libcoot-pli.lai /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-pli.la libtool: install: /usr/bin/install -c .libs/libcoot-pli.a /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-pli.a libtool: install: chmod 644 /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-pli.a libtool: install: ranlib /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/libcoot-pli.a libtool: finish: PATH="/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/home/emsley/bin.Linux:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/home/emsley/molprobity:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /d/emsley/autobuild/install-33-pre-release-gtk3-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pli' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pli' Making install in pyrogen make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pyrogen' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pyrogen' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot" make install-exec-hook make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pyrogen' make[3]: Nothing to be done for `install-exec-hook'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pyrogen' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pyrogen' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pyrogen' Making install in src make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/src' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/src' test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" /bin/sh ../libtool --mode=install /usr/bin/install -c coot-fix-nomenclature-errors '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' /usr/bin/install -c coot coot-density-score-by-residue dynarama '/d/emsley/autobuild/install-33-pre-release-gtk3-python/bin' /usr/bin/install -c coot.py coot.pth '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages' /usr/bin/install -c -m 644 crunch-model.hh '/d/emsley/autobuild/install-33-pre-release-gtk3-python/include/coot' /bin/sh ../libtool --mode=install /usr/bin/install -c coot-bin coot-density-score-by-residue-bin dynarama-bin '/d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec' /usr/bin/install -c -m 644 dynarama.glade '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot' /usr/bin/install -c -m 644 coot.py coot.pth '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages' libtool: install: /usr/bin/install -c coot-fix-nomenclature-errors /d/emsley/autobuild/install-33-pre-release-gtk3-python/bin/coot-fix-nomenclature-errors libtool: install: /usr/bin/install -c coot-bin /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/coot-bin Byte-compiling python modules... coot.py Byte-compiling python modules (optimized versions) ... coot.py libtool: install: /usr/bin/install -c coot-density-score-by-residue-bin /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/coot-density-score-by-residue-bin libtool: install: /usr/bin/install -c dynarama-bin /d/emsley/autobuild/install-33-pre-release-gtk3-python/libexec/dynarama-bin make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/src' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/src' Making install in data make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data' Making install in rama-coeffs make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/rama-coeffs' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/rama-coeffs' make[3]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/rama/zo-tables" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/rama/zo-tables" /usr/bin/install -c -m 644 all-non-pre-pro.tab coeffsolution.dat '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/rama/zo-tables' make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/rama-coeffs' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/rama-coeffs' Making install in cho-models make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-models' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-models' make[3]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/cho-models" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/cho-models" /usr/bin/install -c -m 644 model-level-1-NAG-NAG-ASN-ASN.tab model-level-4-BMA-BETA1-6-BMA.tab model-level-5-MAN-ALPHA1-3-BMA.tab model-level-2-FUC-BETA1-3-NAG.tab model-level-4-BMA-BETA1-6-MAN.tab model-level-5-MAN-ALPHA1-3-MAN.tab model-level-2-FUC-BETA1-6-NAG.tab model-level-4-MAN-ALPHA1-3-BMA.tab model-level-5-MAN-ALPHA1-6-BMA.tab model-level-2-FUL-ALPHA1-3-NAG.tab model-level-4-MAN-ALPHA1-4-BMA.tab model-level-5-MAN-ALPHA1-6-MAN.tab model-level-2-FUL-ALPHA1-6-NAG.tab model-level-4-MAN-ALPHA1-6-BMA.tab model-level-5-NAG-BETA1-2-MAN.tab model-level-2-NAG-BETA1-4-NAG.tab model-level-4-MAN-ALPHA1-6-MAN.tab model-level-6-GAL-BETA1-4-NAG.tab model-level-3-BMA-BETA1-3-NAG.tab model-level-4-NAG-BETA1-4-BMA.tab model-level-6-MAN-ALPHA1-2-MAN.tab model-level-3-BMA-BETA1-4-NAG.tab model-level-5-BMA-BETA1-2-BMA.tab model-level-7-GLC-ALPHA1-3-MAN.tab model-level-3-MAN-ALPHA1-4-NAG.tab model-level-5-BMA-BETA1-6-MAN.tab model-level-4-BMA-BETA1-3-BMA.tab model-level-5-MAN-ALPHA1-2-MAN.tab '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/cho-models' make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-models' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-models' Making install in cho-acedrg make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-acedrg' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-acedrg' make[3]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/cho-acedrg" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/cho-acedrg" /usr/bin/install -c -m 644 BMA-acedrg.cif FUC-acedrg.cif MAN-acedrg.cif NAG-acedrg.cif SIA-acedrg.cif XYP-acedrg.cif '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data/cho-acedrg' make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-acedrg' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data/cho-acedrg' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data' make[3]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data" /usr/bin/install -c -m 644 tutorial-modern.pdb rnasa-1.8-all_refmac1.mtz ligands.db '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/data' make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/data' Making install in man make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/man' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/man' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1" /usr/bin/install -c -m 644 'coot.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot.1' /usr/bin/install -c -m 644 'coot-density-score-by-residue.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-density-score-by-residue.1' /usr/bin/install -c -m 644 'coot-compare-dictionaries.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-compare-dictionaries.1' /usr/bin/install -c -m 644 'coot-available-comp-id.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-available-comp-id.1' /usr/bin/install -c -m 644 'coot-bfactan.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-bfactan.1' /usr/bin/install -c -m 644 'coot-fix-nomenclature-errors.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-fix-nomenclature-errors.1' /usr/bin/install -c -m 644 'coot-make-shelx-restraints.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-make-shelx-restraints.1' /usr/bin/install -c -m 644 'coot-mini-rsr.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/coot-mini-rsr.1' /usr/bin/install -c -m 644 'lidia.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/lidia.1' /usr/bin/install -c -m 644 'findwaters.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/findwaters.1' /usr/bin/install -c -m 644 'findligand.man' '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/man/man1/findligand.1' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/man' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/man' Making install in rama-data make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rama-data' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rama-data' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/rama-data" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/rama-data" /usr/bin/install -c -m 644 rota500-arg.data rota500-asn.data rota500-asp.data rota500-cys.data rota500-gln.data rota500-glu.data rota500-his.data rota500-ile.data rota500-leu.data rota500-lys.data rota500-met.data rota500-phetyr.data rota500-pro.data rota500-ser.data rota500-thr.data rota500-trp.data rota500-val.data '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/rama-data' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rama-data' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rama-data' Making install in doc make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/doc' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/doc' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/doc' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/doc' Making install in rcrane make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rcrane' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rcrane' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane/data" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane/data" /usr/bin/install -c -m 644 data/bases.pdb data/phosAngleSmoothed.csv data/sugarDists.csv data/c2p.pdb data/phosDistSmoothed.csv data/sugarPhosSugarAngleSmoothed.csv data/c3p.pdb data/pseudoChiSmoothed.csv data/thetaEtaClusts.csv data/dihedData.csv data/smoothedPuckerDist.csv data/endingPDists.csv data/startingPDists.csv '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane/data' /usr/bin/install -c -m 644 CHANGELOG.txt buildPhosOxy.py installRCrane.py pseudoMolecule.py selectMapDialog.py LICENSE.txt calcCoords.py launch.py pseudoPredictor.py settings.py chain.py linearInterp.py puckerList.py smoothProb.py NOTICE.txt citationPopup.py logo.svg reviewSuitesGui.py stats.py README.txt coot_gui_adapter.py menu.py revisionNum.py strucCalc.py __init__.py coot_utils_adapter.py nextPhos.py rotData.py suite.py about.py nucleotide.py rotamerSeq.py thetaEtaPredictor.py bondLength.py guiUtils.py phenixRestraints.py rotamerize.py traceGui.py buildInitSugar.py icon.svg '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane' /usr/bin/install -c -m 644 preLaunchCheck.py safelog.py extendChain.py reportInputErrors.py '/d/emsley/autobuild/install-33-pre-release-gtk3-python/lib/python3.6/site-packages/coot/rcrane' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rcrane' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/rcrane' Making install in pixmaps make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps' Making install in icons make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps/icons' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps/icons' 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 $icon | cut -d_ -f4`; \ mkdir -p /d/emsley/autobuild/install-33-pre-release-gtk3-python/share/icons/$THEME/$SIZE/$CONTEXT; \ /usr/bin/install -c -m 644 ./$icon /d/emsley/autobuild/install-33-pre-release-gtk3-python/share/icons/$THEME/$SIZE/$CONTEXT/$ICONFILE; \ done; make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps/icons' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps/icons' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps' make[3]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps" /usr/bin/install -c -m 644 coot-0.8.9.1.png add-alt-conf.png dna.svg probe-clash.svg add-alt-conf.svg edit-backbone.svg radacina_handcuffs-small.svg add-peptide-1.png edit-chi.png ramachandran.png add-peptide-1.svg edit-chi.svg refine-1.svg add-water.svg emsley.jpg refine.png anchor.svg env-distances.png regularize-1.svg aniso-atom.png env-distances.svg regularize.png aniso-atom.svg eugene.jpg renumber-residues.svg appointment-new.png flip-peptide.png reset-view-32.png atom-at-pointer.png flip-peptide.svg reset-view-32.svg atom-at-pointer.svg generic-display-objects.svg reset-view.png auto-fit-rotamer.png geom.svg reset-view.svg auto-fit-rotamer.svg ghosts.png residue-info.png '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps' /usr/bin/install -c -m 644 azerbaijan2.svg ghosts.svg residue-info.svg azerbaijan.svg gln-asn-b-factors.svg rigid-body.png calculate-ghosts.svg gln-asn-b-factorssvg.svg rigid-body.svg cell+symm.png glyco-structures.svg rotamers.png cell+symm.svg gnome-run.png rotamers.svg change-chain-id.svg go-to-atom.svg rtz.png rrz.png chiral.png go-to-ligand.svg rtz.svg rrz.svg chiral.svg gtk-connect-16.png scroll-wheel.svg connect-to-ccp4.svg gtk-font.png secondary-structure.svg connect-to-oca.svg gtk-open-16.png sequence-view.png connect-to-usf.svg gtk-open-24.png sequence-view.svg connect-to-world.svg gtk-open.png side-chain-180.png kevin.jpg side-chain-180.svg '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps' /usr/bin/install -c -m 644 kevin-orig.jpg smiles.png kleywegt.svg smiles.svg map.svg spin-view.png coot-favicon.png merge-molecules.svg spin-view.svg coot-icon.png mutate-auto-fit.svg stereo-view.svg coot-save.png mutate.svg stop.svg coot-save-symm.png panel-screenshot.png temperature.png crosshairs.png peptide-omega.png temperature.svg crosshairs.svg peptide-omega.svg torsion-general.svg delete.png phenixed.svg undo-1.png delete.svg pink-pointer.png undo-1.svg density-fit.svg pink-pointer.svg unknown-blob.png diff-map.png plane-distances.png unknown-blob.svg diff-map.svg plane-distances.svg water-diff-map.svg display-manager.png '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps' /usr/bin/install -c -m 644 pointer-distances.png water-drop.svg display-manager.svg pointer-distances.svg koppi-green-tick-64.png rygle-red-cross-64.png forest51690-dwcheckno-incomplete-64.png go-to-ligand.png go-to-atom.png azerbaijan.png add-water.png mutate.png mutate-auto-fit.png edit-backbone.png torsion-general.png anchor.png regularize-1.png refine-1.png stock-zoom-follow-window-12.svg stock-zoom-follow-window-12.png rama_all.png rama_gly.png rama_pro.png rama_non_gly_pro.png '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot/pixmaps' make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre/pixmaps' make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre' make[2]: Nothing to be done for `install-exec-am'. test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/appdata" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/appdata" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/applications" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/applications" test -z "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" || /usr/bin/mkdir -p "/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot" /usr/bin/install -c -m 644 coot.appdata.xml '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/appdata' /usr/bin/install -c -m 644 coot.desktop '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/applications' /usr/bin/install -c -m 644 cootrc standard-residues.pdb colours.def mtrix-to-ncs-matrix.awk syminfo.lib '/d/emsley/autobuild/install-33-pre-release-gtk3-python/share/coot' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2018-04-29__T16_10_57/coot-0.8.9.2-pre'