Login Name Tty Idle Login Time Office Office Phone Host ana Ana Casañal pts/89 63d Sep 25 12:32 (:1) ana Ana Casañal tty2 165d Sep 25 12:28 (:1) ana Ana Casañal pts/90 63d Sep 25 12:34 (:1) emsley Paul Emsley tty1 165d Jul 8 20:10 (:0) emsley Paul Emsley pts/0 57d Jul 8 20:11 (:0) emsley Paul Emsley pts/1 114d Jul 8 20:23 (:0) emsley Paul Emsley pts/2 40d Jul 8 21:14 (:0) emsley Paul Emsley pts/3 41d Jul 8 22:02 (:0) emsley Paul Emsley pts/4 2d Jul 10 16:00 (:0) emsley Paul Emsley pts/5 139d Jul 8 22:44 (:0) emsley Paul Emsley pts/6 2d Jul 10 19:03 (:0) emsley Paul Emsley pts/7 92d Aug 27 15:21 (:0) emsley Paul Emsley pts/8 139d Jul 10 17:37 (:0) emsley Paul Emsley pts/12 111d Jul 10 17:39 (:0) emsley Paul Emsley pts/13 1:41 Oct 10 19:44 (:0) emsley Paul Emsley pts/15 139d Jul 10 19:15 (:0) emsley Paul Emsley pts/16 138d Jul 10 19:28 (:0) emsley Paul Emsley pts/20 8d Jul 11 16:38 (:0) emsley Paul Emsley pts/21 97d Jul 11 16:49 (:0) emsley Paul Emsley pts/22 1d Oct 10 20:30 (:0) emsley Paul Emsley pts/23 97d Aug 22 14:58 (:0) emsley Paul Emsley pts/24 47d Oct 10 17:21 (:0) emsley Paul Emsley pts/25 133d Jul 16 21:07 (:0) emsley Paul Emsley pts/26 13d Oct 14 18:49 (:0) emsley Paul Emsley pts/27 43d Aug 30 14:38 (:0) emsley Paul Emsley pts/28 133d Jul 16 21:16 (:0) emsley Paul Emsley pts/29 137d Jul 12 17:02 (:0) emsley Paul Emsley pts/31 137d Jul 12 17:09 (:0) emsley Paul Emsley pts/32 132d Jul 16 22:21 (:0) emsley Paul Emsley pts/30 137d Jul 12 17:05 (:0) emsley Paul Emsley pts/33 123d Jul 26 23:09 (:0) emsley Paul Emsley pts/34 131d Jul 18 17:18 (:0) emsley Paul Emsley pts/18 137d Jul 12 19:05 (:0) emsley Paul Emsley pts/19 2:19 Jul 18 20:09 (:0) emsley Paul Emsley pts/35 126d Jul 19 17:54 (:0) emsley Paul Emsley pts/36 123d Jul 19 16:55 (:0) emsley Paul Emsley pts/37 123d Jul 19 17:04 (:0) emsley Paul Emsley pts/38 120d Jul 19 17:05 (:0) emsley Paul Emsley pts/39 1:22 Aug 6 15:42 (:0) emsley Paul Emsley pts/40 124d Jul 25 15:30 (:0) emsley Paul Emsley pts/41 119d Jul 25 20:08 (:0) emsley Paul Emsley pts/42 112d Jul 26 15:28 (:0) emsley Paul Emsley pts/43 124d Jul 26 15:35 (:0) emsley Paul Emsley pts/44 110d Jul 30 13:49 (:0) emsley Paul Emsley pts/45 112d Jul 30 19:54 (:0) emsley Paul Emsley pts/46 119d Jul 30 20:01 (:0) emsley Paul Emsley pts/48 81d Aug 27 15:23 (:0) emsley Paul Emsley pts/49 15d Sep 30 20:17 (:0) emsley Paul Emsley pts/50 56d Oct 2 15:53 (:0) emsley Paul Emsley pts/51 110d Aug 1 19:31 (:0) emsley Paul Emsley pts/52 110d Aug 1 20:57 (:0) emsley Paul Emsley pts/53 96d Aug 8 20:19 (:0) emsley Paul Emsley pts/47 107d Aug 6 21:42 (:0) emsley Paul Emsley pts/54 107d Aug 6 21:51 (:0) emsley Paul Emsley pts/55 16d Oct 10 20:36 (:0) emsley Paul Emsley pts/56 2:16 Oct 14 14:07 (:0) emsley Paul Emsley pts/57 107d Aug 8 19:28 (:0) emsley Paul Emsley pts/58 106d Aug 8 19:29 (:0) emsley Paul Emsley pts/59 43d Oct 14 14:13 (:0) emsley Paul Emsley pts/60 96d Aug 8 20:05 (:0) emsley Paul Emsley pts/61 107d Aug 12 13:28 (:0) emsley Paul Emsley pts/62 44d Oct 14 14:26 (:0) emsley Paul Emsley pts/63 43d Aug 30 14:53 (:0) emsley Paul Emsley pts/64 96d Aug 12 14:52 (:0) emsley Paul Emsley pts/65 99d Aug 12 17:20 (:0) emsley Paul Emsley pts/66 13d Sep 30 15:36 (:0) emsley Paul Emsley pts/67 43d Oct 15 13:07 (:0) emsley Paul Emsley pts/68 16d Oct 15 17:14 (emsley-vm-ubuntu2.lmb.internal) emsley Paul Emsley pts/71 1:24 Aug 16 18:05 (:0) emsley Paul Emsley pts/69 19d Oct 15 13:56 (:0) emsley Paul Emsley pts/70 21d Oct 17 16:42 (:0) emsley Paul Emsley pts/72 44d Oct 14 15:15 (:0) emsley Paul Emsley pts/74 40d Oct 17 18:12 (:0) emsley Paul Emsley pts/75 16d Nov 8 13:24 (:0) emsley Paul Emsley pts/76 82d Sep 6 13:42 (:0) emsley Paul Emsley pts/77 81d Sep 6 17:52 (:0) emsley Paul Emsley pts/78 60d Sep 6 19:09 (:0) emsley Paul Emsley pts/79 78d Sep 6 19:23 (:0) emsley Paul Emsley pts/80 40d Oct 3 10:24 (:0) emsley Paul Emsley pts/83 75d Sep 11 15:36 (:0) emsley Paul Emsley pts/84 13d Oct 17 22:24 (:0) emsley Paul Emsley pts/85 75d Sep 12 20:15 (:0) emsley Paul Emsley pts/86 74d Sep 13 15:42 (:0) emsley Paul Emsley pts/87 5d Nov 11 17:40 (:0) emsley Paul Emsley pts/88 71d Sep 13 20:37 (:0) emsley Paul Emsley pts/81 6d Oct 17 21:29 (:0) emsley Paul Emsley pts/82 54d Oct 3 19:01 (:0) emsley Paul Emsley pts/91 5d Nov 8 14:10 (:0) emsley Paul Emsley pts/92 1 Nov 8 17:46 (:0) emsley Paul Emsley pts/93 2:46 Nov 11 12:13 (:0) emsley Paul Emsley pts/94 13d Nov 13 14:44 (:0) emsley Paul Emsley pts/95 2d Nov 18 15:22 (:0) emsley Paul Emsley pts/96 6d Nov 11 20:10 (hal.lmb.internal) emsley Paul Emsley pts/97 8d Nov 18 19:49 (:0) emsley Paul Emsley pts/98 1d Nov 25 16:17 (hex.lmb.internal) emsley Paul Emsley pts/99 1d Nov 25 17:13 (:0) emsley Paul Emsley pts/100 Nov 25 17:45 (:0) emsley Paul Emsley pts/101 2:46 Nov 27 13:11 (:0) From tar file: /home/emsley/autobuild/building/sources/coot-0.9-pre-revision-9658.tar.gz building in: /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre CFLAGS: CXXFLAGS: -g -O CPPFLAGS: LDFLAGS: PATH: /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin:/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin:/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2/bin:/home/emsley/bin.Linux:/home/emsley/ninja/bin:/home/emsley/vim/bin:/home/emsley/git/bin:/home/emsley/gqview/bin:/home/emsley/gdb/bin:/home/emsley/bin:/home/emsley/tools/bin:/sbin:/usr/sbin:/usr/lib/cups/filter:/home/emsley/molprobity:/home/emsley/bin.Linux:/home/emsley/ninja/bin:/home/emsley/vim/bin:/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:/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc using this guile: /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin/guile ./configure --prefix=/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python --with-fftw-prefix=/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python --with-goocanvas-prefix=/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python --with-glut-prefix=/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python COOT_BUILD_INFO_STRING=built by: Paul Emsley build-host: charybdis on: Wed 27 Nov 1558.16 GMT 2019 --with-boost= --with-guile --with-guile-gtk --with-guile-gtk-prefix=/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python --with-python --with-pygtk --with-modern-language-tools --disable-shared checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... 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 how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop 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 dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking 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 how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 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 whether g++ supports C++11 features by default... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking for std::thread in thread... yes 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 LIBPNG... yes checking for CAIRO... yes checking for SQLite3... no checking for mmdb2... yes checking for ssm... yes no checking for non-prefixed single-precision FFTW2 (fftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin/guile checking for guile-config... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin/guile-config checking for guile-tools... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin/guile-tools checking libguile compile flags... -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -P -pthread checking libguile link flags... -P -pthread -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lguile -lltdl -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lgmp -lcrypt -lm -lltdl checking for Guile-Lib... yes checking for guile-gui... yes checking GUILE_VERSION: 1.8 checking for gsl-config... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 PYGTK... yes Good we have pygtk checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for guile-gtk... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python checking for boostlib >= (102000)... yes checking for python2.7... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/bin/python2.7 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include/python2.7 checking for Python library path... -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lpython2.7 checking for Python site-packages path... /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... yes checking whether boost_python is the correct library... yes checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... 7.65.3 checking build type... Linux-x86_64-scientific-linux-7.6-python-gtk2 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating macros/Makefile config.status: creating pdb-templates/Makefile config.status: creating scheme/Makefile config.status: creating python/Makefile config.status: creating compat/Makefile config.status: creating utils/Makefile config.status: creating coot-utils/Makefile config.status: creating protein_db/Makefile config.status: creating ccp4mg-utils/Makefile config.status: creating coords/Makefile config.status: creating db-main/Makefile config.status: creating density-contour/Makefile config.status: creating surface/Makefile config.status: creating coot-surface/Makefile config.status: creating angles/Makefile config.status: creating mini-mol/Makefile config.status: creating skeleton/Makefile config.status: creating ligand/Makefile config.status: creating geometry/Makefile config.status: creating ideal/Makefile config.status: creating build/Makefile config.status: creating analysis/Makefile config.status: creating high-res/Makefile config.status: creating tw/Makefile config.status: creating cootaneer/Makefile config.status: creating cootilus/Makefile config.status: creating greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating lidia-core/Makefile config.status: creating libgtkgraph/Makefile config.status: creating goograph/Makefile config.status: creating lbg/Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/coot config.status: creating python/coot_load_modules.py config.status: creating data/Makefile config.status: creating data/rama-coeffs/Makefile config.status: creating data/metal/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 fonts/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 Making all in auxil make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil' Making all in catcheck make[2]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/catcheck' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/catcheck' Making all in rama make[2]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/rama' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/rama' Making all in sec-str make[2]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/sec-str' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/strand-analysis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/strand-analysis' Making all in vectors make[2]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/vectors' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil/vectors' make[2]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil' make[1]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/auxil' Making all in scheme make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/scheme' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/scheme' Making all in python make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/python' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/python' Making all in pdb-templates make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/pdb-templates' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/pdb-templates' Making all in macros make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/macros' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/macros' Making all in compat make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/compat' /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -g -O2 -Wall -Wunused -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o mv -f .deps/getopt1.Tpo .deps/getopt1.Plo mv -f .deps/getopt.Tpo .deps/getopt.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Wall -Wunused -o libcoot-compat.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/compat' Making all in utils make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/utils' /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" 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-I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c atomic-numbers.cc -o atomic-numbers.o libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT hsv-rgb.lo -MD -MP -MF .deps/hsv-rgb.Tpo -c hsv-rgb.cc -o hsv-rgb.o mv -f .deps/win-compat.Tpo .deps/win-compat.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT align-utils.lo -MD -MP -MF .deps/align-utils.Tpo -c align-utils.cc -o align-utils.o mv -f .deps/threads.Tpo .deps/threads.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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/hsv-rgb.Tpo .deps/hsv-rgb.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT split-indices.lo -MD -MP -MF .deps/split-indices.Tpo -c -o split-indices.lo split-indices.cc libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT split-indices.lo -MD -MP -MF .deps/split-indices.Tpo -c split-indices.cc -o split-indices.o mv -f .deps/coot-fasta.Tpo .deps/coot-fasta.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT radix.lo -MD -MP -MF .deps/radix.Tpo -c -o radix.lo radix.cc mv -f .deps/atomic-numbers.Tpo .deps/atomic-numbers.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT logging.lo -MD -MP -MF .deps/logging.Tpo -c -o logging.lo logging.cc libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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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"-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT logging.lo -MD -MP -MF .deps/logging.Tpo -c logging.cc -o logging.o mv -f .deps/align-utils.Tpo .deps/align-utils.Plo mv -f .deps/dodec.Tpo .deps/dodec.Plo mv -f .deps/radix.Tpo .deps/radix.Plo mv -f .deps/split-indices.Tpo .deps/split-indices.Plo mv -f .deps/pir-alignment.Tpo .deps/pir-alignment.Plo mv -f .deps/logging.Tpo .deps/logging.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++ -std=gnu++11 -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-utils.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 split-indices.lo radix.lo logging.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 split-indices.o radix.o logging.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 `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/utils' Making all in protein_db make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/protein_db' /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" 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-DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 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++ -std=gnu++11 -g -O -Wall -Wno-unused -o libcoot-protein-db.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib protein_db.lo protein_db_utils.lo rna_db.lo -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/protein_db' Making all in mini-mol make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/mini-mol' /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -g -O -Wall -Wno-unused -o libcoot-mini-mol.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lmmdb2 -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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 `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/mini-mol' Making all in geometry make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/geometry' /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c -o protein-geometry.lo protein-geometry.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c -o protein-geometry-mmdb.lo protein-geometry-mmdb.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c -o read-sbase.lo read-sbase.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c -o energy-lib.lo energy-lib.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 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compare-dictionaries.o compare-dictionaries.cc libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT mol-utils-2.lo -MD -MP -MF .deps/mol-utils-2.Tpo -c mol-utils-2.cc -o mol-utils-2.o mv -f .deps/mol-utils-2.Tpo .deps/mol-utils-2.Plo g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT make-shelx-restraints.o -MD -MP -MF .deps/make-shelx-restraints.Tpo -c -o make-shelx-restraints.o make-shelx-restraints.cc mv -f .deps/residue-and-atom-specs.Tpo .deps/residue-and-atom-specs.Plo g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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/chem_mods.Tpo .deps/chem_mods.Plo 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/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++ -std=gnu++11 -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-geometry.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo mol-utils.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/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lmmdb2 libtool: link: ar cru .libs/libcoot-geometry.a protein-geometry.o protein-geometry-mmdb.o read-sbase.o energy-lib.o mol-utils.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++ -std=gnu++11 -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o ./libcoot-geometry.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lmmdb2 /bin/sh ../libtool --tag=CXX --mode=link g++ -std=gnu++11 -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o coot-make-shelx-restraints make-shelx-restraints.o ./libcoot-geometry.la ../utils/libcoot-utils.la -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 /bin/sh ../libtool --tag=CXX --mode=link g++ -std=gnu++11 -DDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share"' -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o coot-available-comp-id available-comp-id.o ./libcoot-geometry.la libtool: link: g++ -std=gnu++11 -DDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-available-comp-id available-comp-id.o ./.libs/libcoot-geometry.a -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/mini-mol/.libs/libcoot-mini-mol.a /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/utils/.libs/libcoot-utils.a /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-ccp4.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-cif.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-minimol.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-mmdb.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-cns.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-phs.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-contrib.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-core.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/librfftw.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libfftw.so -lm -lpthread /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libccp4c.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -Wl,-rpath -Wl,/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib libtool: link: g++ -std=gnu++11 -DDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o ./.libs/libcoot-geometry.a -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/mini-mol/.libs/libcoot-mini-mol.a /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/utils/.libs/libcoot-utils.a /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-ccp4.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-cif.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-minimol.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-mmdb.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-cns.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-phs.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-contrib.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-core.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/librfftw.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libfftw.so -lm -lpthread /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libccp4c.so ../utils/.libs/libcoot-utils.a ../compat/.libs/libcoot-compat.a /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -Wl,-rpath -Wl,/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib libtool: link: g++ -std=gnu++11 -DDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-make-shelx-restraints make-shelx-restraints.o ./.libs/libcoot-geometry.a -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/mini-mol/.libs/libcoot-mini-mol.a /home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/utils/.libs/libcoot-utils.a ../utils/.libs/libcoot-utils.a /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-ccp4.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-cif.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-minimol.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-mmdb.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-cns.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-phs.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-contrib.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libclipper-core.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/librfftw.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libfftw.so -lm -lpthread /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libccp4c.so /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -Wl,-rpath -Wl,/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib make[1]: Leaving directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/geometry' Making all in lidia-core make[1]: Entering directory `/home/emsley/autobuild/building/charybdis_2019-11-27__T15_57_12/coot-0.9-pre/lidia-core' /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-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++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c -o lbg-molfile.lo lbg-molfile.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 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-I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c -o coot-fffear.lo coot-fffear.cc libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c coot-fffear.cc -o coot-fffear.o mv -f .deps/coot-coord-extras.Tpo .deps/coot-coord-extras.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT spherical-harmonics.lo -MD -MP -MF .deps/spherical-harmonics.Tpo -c -o spherical-harmonics.lo spherical-harmonics.cc libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT spherical-harmonics.lo -MD -MP -MF .deps/spherical-harmonics.Tpo -c spherical-harmonics.cc -o spherical-harmonics.o mv -f .deps/xmap-stats.Tpo .deps/xmap-stats.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT segmap.lo -MD -MP -MF .deps/segmap.Tpo -c -o segmap.lo segmap.cc libtool: compile: g++ -std=gnu++11 -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9-pre\" "-DPACKAGE_STRING=\"coot 0.9-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9-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 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT segmap.lo -MD -MP -MF .deps/segmap.Tpo -c segmap.cc -o segmap.o mv -f .deps/peak-search.Tpo .deps/peak-search.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -std=gnu++11 -DHAVE_GSL -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lmmdb2 -o libcoot-coord-utils.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo glyco-torsions.lo coot-least-squares.lo atom-overlaps.lo reduce.lo atom-selection-container.lo contact-info.lo coot-shelx-ins.lo secondary-structure-headers.lo plane-utils.lo c-beta-deviations.lo lidia-core-functions.lo atom-tools.lo bonded-atoms.lo bricks.lo helix-like.lo merge-atom-selections.lo contacts-by-bricks.lo stack-and-pair.lo ../lidia-core/libcoot-lidia-core.la ../geometry/libcoot-geometry.la -L/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib -lgsl -lgslcblas -lm -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil mv -f .deps/spherical-harmonics.Tpo .deps/spherical-harmonics.Plo mv -f .deps/coot-coord-utils-glyco.Tpo .deps/coot-coord-utils-glyco.Plo libtool: link: ar cru .libs/libcoot-coord-utils.a coot-coord-utils.o coot-coord-utils-nucleotides.o coot-rama.o coot-h-bonds.o hole.o read-sm-cif.o bonded-pairs.o helix-analysis.o elastic.o glyco-torsions.o coot-least-squares.o atom-overlaps.o reduce.o atom-selection-container.o contact-info.o coot-shelx-ins.o secondary-structure-headers.o plane-utils.o c-beta-deviations.o lidia-core-functions.o atom-tools.o bonded-atoms.o bricks.o helix-like.o merge-atom-selections.o contacts-by-bricks.o stack-and-pair.o libtool: link: ranlib .libs/libcoot-coord-utils.a libtool: link: ( cd ".libs" && rm -f "libcoot-coord-utils.la" && ln -s "../libcoot-coord-utils.la" "libcoot-coord-utils.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -std=gnu++11 -DHAVE_GSL -DPKGDATADIR='"/home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-coord-extras.la -rpath /home/emsley/autobuild/Linux-charybdis-pre-release-gtk2-python/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo jed-flip.lo libcoot-coord-utils.la libtool: link: ar cru .libs/libcoot-coord-extras.a coot-coord-extras.o coot-coord-lsq.o coot-tree-extras.o water-coordination.o lsq-improve.o coot-coord-utils-glyco.o jed-flip.o libtool: link: ranlib .libs/libcoot-coord-extras.a libtool: link: ( cd ".libs" && rm -f "libcoot-coord-extras.la" && ln -s "../libcoot-coord-extras.la" "libcoot-coord-extras.la" ) mv -f .deps/segmap.Tpo .deps/segmap.Plo mv -f .deps/coot-map-heavy.Tpo .deps/coot-map-heavy.Plo mv -f .deps/maps-spherical.Tpo .deps/maps-spherical.Plo mv -f .deps/coot-fffear.Tpo .deps/coot-fffear.Plo make[1]: *** [coot-map-utils.lo] Error 1 make: *** [all-recursive] Interrupt