Login Name Tty Idle Login Time Office Office Phone Host ana Ana Casañal pts/89 99d Sep 25 12:32 (:1) ana Ana Casañal tty2 201d Sep 25 12:28 (:1) ana Ana Casañal pts/90 99d Sep 25 12:34 (:1) emsley Paul Emsley tty1 201d Jul 8 20:10 (:0) emsley Paul Emsley pts/0 30d Jul 8 20:11 (:0) emsley Paul Emsley pts/2 Jan 2 11:52 (atg.lmb.internal) emsley Paul Emsley pts/1 150d Jul 8 20:23 (:0) emsley Paul Emsley pts/3 77d Jul 8 22:02 (:0) emsley Paul Emsley pts/5 175d Jul 8 22:44 (:0) emsley Paul Emsley pts/7 128d Aug 27 15:21 (:0) emsley Paul Emsley pts/8 176d Jul 10 17:37 (:0) emsley Paul Emsley pts/12 147d Jul 10 17:39 (:0) emsley Paul Emsley pts/13 22d Oct 10 19:44 (:0) emsley Paul Emsley pts/15 175d Jul 10 19:15 (:0) emsley Paul Emsley pts/16 174d Jul 10 19:28 (:0) emsley Paul Emsley pts/21 133d Jul 11 16:49 (:0) emsley Paul Emsley pts/22 37d Oct 10 20:30 (:0) emsley Paul Emsley pts/23 133d Aug 22 14:58 (:0) emsley Paul Emsley pts/24 84d Oct 10 17:21 (:0) emsley Paul Emsley pts/25 169d Jul 16 21:07 (:0) emsley Paul Emsley pts/26 49d Oct 14 18:49 (:0) emsley Paul Emsley pts/27 79d Aug 30 14:38 (:0) emsley Paul Emsley pts/28 169d Jul 16 21:16 (:0) emsley Paul Emsley pts/29 173d Jul 12 17:02 (:0) emsley Paul Emsley pts/31 174d Jul 12 17:09 (:0) emsley Paul Emsley pts/32 168d Jul 16 22:21 (:0) emsley Paul Emsley pts/30 174d Jul 12 17:05 (:0) emsley Paul Emsley pts/33 159d Jul 26 23:09 (:0) emsley Paul Emsley pts/34 167d Jul 18 17:18 (:0) emsley Paul Emsley pts/18 173d Jul 12 19:05 (:0) emsley Paul Emsley pts/35 162d Jul 19 17:54 (:0) emsley Paul Emsley pts/36 159d Jul 19 16:55 (:0) emsley Paul Emsley pts/37 159d Jul 19 17:04 (:0) emsley Paul Emsley pts/38 156d Jul 19 17:05 (:0) emsley Paul Emsley pts/39 22d Dec 10 19:07 (:0) emsley Paul Emsley pts/40 160d Jul 25 15:30 (:0) emsley Paul Emsley pts/41 156d Jul 25 20:08 (:0) emsley Paul Emsley pts/42 148d Jul 26 15:28 (:0) emsley Paul Emsley pts/43 160d Jul 26 15:35 (:0) emsley Paul Emsley pts/44 146d Jul 30 13:49 (:0) emsley Paul Emsley pts/45 148d Jul 30 19:54 (:0) emsley Paul Emsley pts/46 155d Jul 30 20:01 (:0) emsley Paul Emsley pts/48 118d Aug 27 15:23 (:0) emsley Paul Emsley pts/49 51d Sep 30 20:17 (:0) emsley Paul Emsley pts/50 92d Oct 2 15:53 (:0) emsley Paul Emsley pts/51 146d Aug 1 19:31 (:0) emsley Paul Emsley pts/52 146d Aug 1 20:57 (:0) emsley Paul Emsley pts/53 133d Aug 8 20:19 (:0) emsley Paul Emsley pts/47 143d Aug 6 21:42 (:0) emsley Paul Emsley pts/54 143d Aug 6 21:51 (:0) emsley Paul Emsley pts/55 52d Oct 10 20:36 (:0) emsley Paul Emsley pts/56 31d Oct 14 14:07 (:0) emsley Paul Emsley pts/57 143d Aug 8 19:28 (:0) emsley Paul Emsley pts/58 143d Aug 8 19:29 (:0) emsley Paul Emsley pts/59 79d Oct 14 14:13 (:0) emsley Paul Emsley pts/60 133d Aug 8 20:05 (:0) emsley Paul Emsley pts/61 143d Aug 12 13:28 (:0) emsley Paul Emsley pts/62 80d Oct 14 14:26 (:0) emsley Paul Emsley pts/63 79d Aug 30 14:53 (:0) emsley Paul Emsley pts/64 132d Aug 12 14:52 (:0) emsley Paul Emsley pts/65 135d Aug 12 17:20 (:0) emsley Paul Emsley pts/66 49d Sep 30 15:36 (:0) emsley Paul Emsley pts/67 79d Oct 15 13:07 (:0) emsley Paul Emsley pts/68 52d Oct 15 17:14 (emsley-vm-ubuntu2.lmb.internal) emsley Paul Emsley pts/71 22d Aug 16 18:05 (:0) emsley Paul Emsley pts/69 55d Oct 15 13:56 (:0) emsley Paul Emsley pts/70 57d Oct 17 16:42 (:0) emsley Paul Emsley pts/72 80d Oct 14 15:15 (:0) emsley Paul Emsley pts/74 76d Oct 17 18:12 (:0) emsley Paul Emsley pts/75 52d Nov 8 13:24 (:0) emsley Paul Emsley pts/76 118d Sep 6 13:42 (:0) emsley Paul Emsley pts/77 118d Sep 6 17:52 (:0) emsley Paul Emsley pts/78 96d Sep 6 19:09 (:0) emsley Paul Emsley pts/79 114d Sep 6 19:23 (:0) emsley Paul Emsley pts/80 76d Oct 3 10:24 (:0) emsley Paul Emsley pts/83 111d Sep 11 15:36 (:0) emsley Paul Emsley pts/84 49d Oct 17 22:24 (:0) emsley Paul Emsley pts/85 111d Sep 12 20:15 (:0) emsley Paul Emsley pts/86 110d Sep 13 15:42 (:0) emsley Paul Emsley pts/87 41d Nov 11 17:40 (:0) emsley Paul Emsley pts/88 107d Sep 13 20:37 (:0) emsley Paul Emsley pts/81 42d Oct 17 21:29 (:0) emsley Paul Emsley pts/82 90d Oct 3 19:01 (:0) emsley Paul Emsley pts/91 41d Nov 8 14:10 (:0) emsley Paul Emsley pts/92 24d Nov 8 17:46 (:0) emsley Paul Emsley pts/93 31d Nov 11 12:13 (:0) emsley Paul Emsley pts/94 49d Nov 13 14:44 (:0) emsley Paul Emsley pts/95 19d Nov 18 15:22 (:0) emsley Paul Emsley pts/97 23d Dec 10 14:09 (:0) emsley Paul Emsley pts/99 37d Nov 25 17:13 (:0) emsley Paul Emsley pts/100 24d Nov 25 17:45 (:0) emsley Paul Emsley pts/101 22d Nov 27 13:11 (:0) emsley Paul Emsley pts/102 24d Dec 2 14:05 (:0) emsley Paul Emsley pts/103 22d Dec 10 19:09 (:0) emsley Paul Emsley pts/98 23d Dec 10 15:22 (:0) emsley Paul Emsley pts/96 23d Dec 10 14:08 (:0) emsley Paul Emsley pts/104 22d Dec 10 19:26 (:0) From tar file: /d/emsley/autobuild/building/sources/coot-0.8.9.3-pre-revision-8034.tar.gz building in: /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre CFLAGS: CXXFLAGS: -g -O CPPFLAGS: LDFLAGS: PATH: /d/emsley/autobuild/install-pre-release-gtk2-python/bin:/d/emsley/autobuild/install-pre-release-gtk2-python/bin:/d/emsley/autobuild/install-pre-release-gtk2/bin:/home/emsley/bin:/home/emsley/ccp4/ccp4-7.0/etc:/home/emsley/ccp4/ccp4-7.0/bin:/d/emsley/ccp4/ccp4-7.0/etc:/d/emsley/ccp4/ccp4-7.0/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:/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-pre-release-gtk2-python/bin/guile ./configure --prefix=/d/emsley/autobuild/install-pre-release-gtk2-python --with-fftw-prefix=/d/emsley/autobuild/install-pre-release-gtk2-python --with-goocanvas-prefix=/d/emsley/autobuild/install-pre-release-gtk2-python --with-glut-prefix=/d/emsley/autobuild/install-pre-release-gtk2-python COOT_BUILD_INFO_STRING=built by: Paul Emsley build-host: charybdis on: Thu 02 Jan 1705.00 GMT 2020 --with-guile --with-guile-gtk --with-guile-gtk-prefix=/d/emsley/autobuild/install-pre-release-gtk2-python --with-python --with-pygtk --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 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 non-prefixed single-precision FFTW2 (fftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile... /d/emsley/autobuild/install-pre-release-gtk2-python/bin/guile checking for guile-config... /d/emsley/autobuild/install-pre-release-gtk2-python/bin/guile-config checking for guile-tools... /d/emsley/autobuild/install-pre-release-gtk2-python/bin/guile-tools checking libguile compile flags... -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -P -pthread checking libguile link flags... -P -pthread -L/d/emsley/autobuild/install-pre-release-gtk2-python/lib -lguile -lltdl -L/d/emsley/autobuild/install-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... /d/emsley/autobuild/install-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... /d/emsley/autobuild/install-pre-release-gtk2-python 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 python2.7... /d/emsley/autobuild/install-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/d/emsley/autobuild/install-pre-release-gtk2-python/include/python2.7 checking for Python library path... -L/d/emsley/autobuild/install-pre-release-gtk2-python/lib -lpython2.7 checking for Python site-packages path... /d/emsley/autobuild/install-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... no checking libglade... no 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/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 Making all in auxil make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' Making all in catcheck make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/catcheck' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/catcheck' Making all in rama make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/rama' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/rama' Making all in sec-str make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/sec-str' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/strand-analysis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/strand-analysis' Making all in vectors make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/vectors' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/vectors' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' Making all in scheme make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/scheme' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/scheme' Making all in python make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python' Making all in pdb-templates make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pdb-templates' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pdb-templates' Making all in macros make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/macros' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/macros' Making all in compat make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/compat' /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O2 -Wall -Wunused -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O2 -Wall -Wunused -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.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 /d/emsley/autobuild/install-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 `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/compat' Making all in utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c -o gdk-keysyms.lo gdk-keysyms.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT hsv-rgb.lo -MD -MP -MF .deps/hsv-rgb.Tpo -c -o hsv-rgb.lo hsv-rgb.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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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-DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT win-compat.lo -MD -MP -MF .deps/win-compat.Tpo -c -o win-compat.lo win-compat.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT threads.lo -MD -MP -MF .deps/threads.Tpo -c -o threads.lo threads.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -o coot-utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c coot-fasta.cc -o coot-fasta.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-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 libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c gdk-keysyms.cc -o gdk-keysyms.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT dodec.lo -MD -MP -MF .deps/dodec.Tpo -c dodec.cc -o dodec.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT win-compat.lo -MD -MP -MF .deps/win-compat.Tpo -c win-compat.cc -o win-compat.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT threads.lo -MD -MP -MF .deps/threads.Tpo -c threads.cc -o threads.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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-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/align-utils.Tpo .deps/align-utils.Plo mv -f .deps/hsv-rgb.Tpo .deps/hsv-rgb.Plo mv -f .deps/coot-fasta.Tpo .deps/coot-fasta.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-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-utils.la -rpath /d/emsley/autobuild/install-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 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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils' Making all in protein_db make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/protein_db' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -g -O -Wall -Wno-unused -o libcoot-protein-db.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-python/lib protein_db.lo protein_db_utils.lo rna_db.lo -L/d/emsley/autobuild/install-pre-release-gtk2-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-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 `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/protein_db' Making all in mini-mol make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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 libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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 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-pre-release-gtk2-python/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -L/d/emsley/autobuild/install-pre-release-gtk2-python/lib -lmmdb2 -L/d/emsley/autobuild/install-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 `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol' Making all in geometry make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/geometry' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT chem_mods.lo -MD -MP -MF .deps/chem_mods.Tpo -c -o chem_mods.lo chem_mods.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT srs-interface.lo -MD -MP -MF .deps/srs-interface.Tpo -c -o srs-interface.lo srs-interface.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT protein-donor-acceptors.lo -MD -MP -MF .deps/protein-donor-acceptors.Tpo -c -o protein-donor-acceptors.lo protein-donor-acceptors.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT lbg-graph.lo -MD -MP -MF .deps/lbg-graph.Tpo -c -o lbg-graph.lo lbg-graph.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-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 protein-geometry-mmdb.cc -o protein-geometry-mmdb.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -o protein-geometry.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c read-sbase.cc -o read-sbase.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT srs-interface.lo -MD -MP -MF .deps/srs-interface.Tpo -c srs-interface.cc -o srs-interface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c energy-lib.cc -o energy-lib.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT lbg-graph.lo -MD -MP -MF .deps/lbg-graph.Tpo -c lbg-graph.cc -o lbg-graph.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT protein-donor-acceptors.lo -MD -MP -MF .deps/protein-donor-acceptors.Tpo -c protein-donor-acceptors.cc -o protein-donor-acceptors.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT chem_mods.lo -MD -MP -MF .deps/chem_mods.Tpo -c chem_mods.cc -o chem_mods.o mv -f .deps/srs-interface.Tpo .deps/srs-interface.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT dreiding.lo -MD -MP -MF .deps/dreiding.Tpo -c -o dreiding.lo dreiding.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT dreiding.lo -MD -MP -MF .deps/dreiding.Tpo -c dreiding.cc -o dreiding.o mv -f .deps/read-sbase.Tpo .deps/read-sbase.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT dict-utils.lo -MD -MP -MF .deps/dict-utils.Tpo -c -o dict-utils.lo dict-utils.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT dict-utils.lo -MD -MP -MF .deps/dict-utils.Tpo -c dict-utils.cc -o dict-utils.o mv -f .deps/protein-geometry-mmdb.Tpo .deps/protein-geometry-mmdb.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT cif-parse.lo -MD -MP -MF .deps/cif-parse.Tpo -c -o cif-parse.lo cif-parse.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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/\" 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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 -DHAVE_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT residue-and-atom-specs.lo -MD -MP -MF .deps/residue-and-atom-specs.Tpo -c residue-and-atom-specs.cc -o residue-and-atom-specs.o mv -f .deps/protein-donor-acceptors.Tpo .deps/protein-donor-acceptors.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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 -o mol-utils-2.lo mol-utils-2.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-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/main-chain.Tpo .deps/main-chain.Plo g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT compare-dictionaries.o -MD -MP -MF .deps/compare-dictionaries.Tpo -c -o compare-dictionaries.o compare-dictionaries.cc mv -f .deps/mol-utils-2.Tpo .deps/mol-utils-2.Plo g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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/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/make-shelx-restraints.Tpo .deps/make-shelx-restraints.Po mv -f .deps/compare-dictionaries.Tpo .deps/compare-dictionaries.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-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-geometry.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-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-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 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-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o ./libcoot-geometry.la ../compat/libcoot-compat.la ../utils/libcoot-utils.la -L/d/emsley/autobuild/install-pre-release-gtk2-python/lib -lmmdb2 /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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/d/emsley/autobuild/install-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++ -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o ./.libs/libcoot-geometry.a -L/d/emsley/autobuild/install-pre-release-gtk2-python/lib -L=/d/emsley/autobuild/install-pre-release-gtk2-python/lib:-L/d/emsley/autobuild/install-pre-release-gtk2-python/lib: /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol/.libs/libcoot-mini-mol.a /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-ccp4.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-cif.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-minimol.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-mmdb.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-cns.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-phs.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-contrib.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-core.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/librfftw.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libfftw.so -lm -lpthread /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4c.so ../compat/.libs/libcoot-compat.a ../utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/d/emsley/autobuild/install-pre-release-gtk2-python/lib -Wl,-rpath -Wl,/d/emsley/autobuild/install-pre-release-gtk2-python/lib libtool: link: g++ -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-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/d/emsley/autobuild/install-pre-release-gtk2-python/lib -L=/d/emsley/autobuild/install-pre-release-gtk2-python/lib:-L/d/emsley/autobuild/install-pre-release-gtk2-python/lib: /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol/.libs/libcoot-mini-mol.a /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-ccp4.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-cif.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-minimol.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-mmdb.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-cns.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-phs.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-contrib.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-core.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/librfftw.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libfftw.so -lm -lpthread /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4c.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/d/emsley/autobuild/install-pre-release-gtk2-python/lib -Wl,-rpath -Wl,/d/emsley/autobuild/install-pre-release-gtk2-python/lib libtool: link: g++ -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -DPKGDATADIR=\"/d/emsley/autobuild/install-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/d/emsley/autobuild/install-pre-release-gtk2-python/lib -L=/d/emsley/autobuild/install-pre-release-gtk2-python/lib:-L/d/emsley/autobuild/install-pre-release-gtk2-python/lib: /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol/.libs/libcoot-mini-mol.a /d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils/.libs/libcoot-utils.a ../utils/.libs/libcoot-utils.a /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-ccp4.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-cif.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-minimol.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-mmdb.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-cns.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-phs.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-contrib.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libclipper-core.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/librfftw.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libfftw.so -lm -lpthread /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4c.so /d/emsley/autobuild/install-pre-release-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/d/emsley/autobuild/install-pre-release-gtk2-python/lib -Wl,-rpath -Wl,/d/emsley/autobuild/install-pre-release-gtk2-python/lib make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/geometry' Making all in coot-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-utils' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-coord-utils.lo -MD -MP -MF .deps/coot-coord-utils.Tpo -c -o coot-coord-utils.lo coot-coord-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL 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-I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT bonded-pairs.lo -MD -MP -MF .deps/bonded-pairs.Tpo -c -o bonded-pairs.lo bonded-pairs.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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 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helix-analysis.cc -o helix-analysis.o mv -f .deps/helix-analysis.Tpo .deps/helix-analysis.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT elastic.lo -MD -MP -MF .deps/elastic.Tpo -c -o elastic.lo elastic.cc mv -f .deps/coot-rama.Tpo .deps/coot-rama.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include 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-I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-least-squares.lo -MD -MP -MF .deps/coot-least-squares.Tpo -c -o coot-least-squares.lo coot-least-squares.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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 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-I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT plane-utils.lo -MD -MP -MF .deps/plane-utils.Tpo -c plane-utils.cc -o plane-utils.o mv -f .deps/hole.Tpo .deps/hole.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-shelx-ins.lo -MD -MP -MF .deps/coot-shelx-ins.Tpo -c -o coot-shelx-ins.lo coot-shelx-ins.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-shelx-ins.lo -MD -MP -MF .deps/coot-shelx-ins.Tpo -c coot-shelx-ins.cc -o coot-shelx-ins.o mv -f .deps/secondary-structure-headers.Tpo .deps/secondary-structure-headers.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c -o coot-coord-extras.lo coot-coord-extras.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c coot-coord-extras.cc -o coot-coord-extras.o mv -f .deps/coot-h-bonds.Tpo .deps/coot-h-bonds.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 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-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c coot-coord-lsq.cc -o coot-coord-lsq.o mv -f .deps/plane-utils.Tpo .deps/plane-utils.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c -o coot-tree-extras.lo coot-tree-extras.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c coot-tree-extras.cc -o coot-tree-extras.o mv -f .deps/glyco-torsions.Tpo .deps/glyco-torsions.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT water-coordination.lo -MD -MP -MF .deps/water-coordination.Tpo -c -o water-coordination.lo water-coordination.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT water-coordination.lo -MD -MP -MF .deps/water-coordination.Tpo -c water-coordination.cc -o water-coordination.o mv -f .deps/coot-coord-lsq.Tpo .deps/coot-coord-lsq.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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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-DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT maps-spherical.lo -MD -MP -MF .deps/maps-spherical.Tpo -c maps-spherical.cc -o maps-spherical.o mv -f .deps/atom-overlaps.Tpo .deps/atom-overlaps.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c -o coot-map-heavy.lo coot-map-heavy.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c coot-map-heavy.cc -o coot-map-heavy.o mv -f .deps/xmap-stats.Tpo .deps/xmap-stats.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/d/emsley/autobuild/install-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/trim.Tpo .deps/trim.Plo mv -f .deps/peak-search.Tpo .deps/peak-search.Plo mv -f .deps/coot-coord-utils-glyco.Tpo .deps/coot-coord-utils-glyco.Plo mv -f .deps/coot-map-heavy.Tpo .deps/coot-map-heavy.Plo mv -f .deps/coot-coord-utils.Tpo .deps/coot-coord-utils.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-coord-utils.la -rpath /d/emsley/autobuild/install-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 secondary-structure-headers.lo plane-utils.lo ../geometry/libcoot-geometry.la -L/d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/lib -lgsl -lgslcblas -lm 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 secondary-structure-headers.o plane-utils.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++ -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-shelx.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-python/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-coord-extras.la -rpath /d/emsley/autobuild/install-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 libcoot-coord-utils.la mv -f .deps/coot-fffear.Tpo .deps/coot-fffear.Plo mv -f .deps/maps-spherical.Tpo .deps/maps-spherical.Plo 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 libtool: link: ar cru .libs/libcoot-shelx.a coot-shelx-ins.o libtool: link: ranlib .libs/libcoot-shelx.a libtool: link: ( cd ".libs" && rm -f "libcoot-shelx.la" && ln -s "../libcoot-shelx.la" "libcoot-shelx.la" ) 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/coot-map-utils.Tpo .deps/coot-map-utils.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-map-utils.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-python/lib coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo libcoot-coord-utils.la -L/d/emsley/autobuild/install-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-map-utils.a coot-map-utils.o peak-search.o peak-search-from-list.o trim.o xmap-stats.o maps-spherical.o libtool: link: ranlib .libs/libcoot-map-utils.a libtool: link: ( cd ".libs" && rm -f "libcoot-map-utils.la" && ln -s "../libcoot-map-utils.la" "libcoot-map-utils.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -g -O -Wall -Wno-unused -o libcoot-map-heavy.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-python/lib coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la -L/d/emsley/autobuild/install-pre-release-gtk2-python/lib -lgsl -lgslcblas -lm libtool: link: ar cru .libs/libcoot-map-heavy.a coot-map-heavy.o coot-fffear.o libtool: link: ranlib .libs/libcoot-map-heavy.a libtool: link: ( cd ".libs" && rm -f "libcoot-map-heavy.la" && ln -s "../libcoot-map-heavy.la" "libcoot-map-heavy.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-utils' Making all in surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/surface' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSphereElement.lo -MD -MP -MF .deps/CXXSphereElement.Tpo -c -o CXXSphereElement.lo CXXSphereElement.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE 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-DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSphereTriangleEdge.lo -MD -MP -MF .deps/CXXSphereTriangleEdge.Tpo -c -o CXXSphereTriangleEdge.lo CXXSphereTriangleEdge.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXCoord.lo -MD -MP -MF .deps/CXXCoord.Tpo -c -o CXXCoord.lo CXXCoord.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c CXXSphereNode.cpp -o CXXSphereNode.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSphereElement.lo -MD -MP -MF .deps/CXXSphereElement.Tpo -c CXXSphereElement.cpp -o CXXSphereElement.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c CXXCircle.cpp -o CXXCircle.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -o CXXChargeTable.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSphereTriangleEdge.lo -MD -MP -MF .deps/CXXSphereTriangleEdge.Tpo -c CXXSphereTriangleEdge.cpp -o CXXSphereTriangleEdge.o In file included from CXXNewHood.h:22:0, from CXXCircle.cpp:12: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ 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 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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c -o CXXSurface.lo CXXSurface.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c CXXSurface.cpp -o CXXSurface.o In file included from CXXNewHood.h:22:0, from CXXSurface.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ CXXSurface.cpp:593:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(nSelAtoms, SelAtom, cout, unitSphereAtOrigin, vdwBallPntrs, contactMap, ContextSelAtom, splitReentrantProbes) schedule(dynamic, 100) //num_threads(2) ^ CXXSurface.cpp:597:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical(cout) ^ CXXSurface.cpp:618:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) ^ mv -f .deps/CXXSphereNode.Tpo .deps/CXXSphereNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXCreator.lo -MD -MP -MF .deps/CXXCreator.Tpo -c -o CXXCreator.lo CXXCreator.cpp mv -f .deps/CXXSphereTriangle.Tpo .deps/CXXSphereTriangle.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXCreator.lo -MD -MP -MF .deps/CXXCreator.Tpo -c CXXCreator.cpp -o CXXCreator.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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/CXXSphereTriangleEdge.Tpo .deps/CXXSphereTriangleEdge.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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]; ^ 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]); ^ mv -f .deps/CXXSurfaceVertex.Tpo .deps/CXXSurfaceVertex.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c -o CXXTorusElement.lo CXXTorusElement.cpp mv -f .deps/CXXException.Tpo .deps/CXXException.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c -o CXXFFTSolventMap.lo CXXFFTSolventMap.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c CXXTorusElement.cpp -o CXXTorusElement.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c CXXFFTSolventMap.cpp -o CXXFFTSolventMap.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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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/CXXTorusNode.Tpo .deps/CXXTorusNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c -o CXXFortranFile.lo CXXFortranFile.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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp -o CXXFortranFile.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c CXXNewHood.cpp -o CXXNewHood.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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c -o CXXNode.lo CXXNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c CXXTriangle.cpp -o CXXTriangle.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c CXXNode.cpp -o CXXNode.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/CXXNode.Tpo .deps/CXXNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c CXXQADSurface.cpp -o CXXQADSurface.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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXBall.lo -MD -MP -MF .deps/CXXBall.Tpo -c CXXBall.cpp -o CXXBall.o In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurface.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ mv -f .deps/CXXTriangle.Tpo .deps/CXXTriangle.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp mv -f .deps/CXXFortranFile.Tpo .deps/CXXFortranFile.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c -o CXXSpace.lo CXXSpace.cpp mv -f .deps/CXXTorusElement.Tpo .deps/CXXTorusElement.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -o CXXQADSurfaceStaticData.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -o CXXSpace.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) ^ libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I../coot-utils -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c CXXUtils.cpp -o CXXUtils.o In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurfaceStaticData.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ mv -f .deps/CXXCircleNode.Tpo .deps/CXXCircleNode.Plo mv -f .deps/CXXSpace.Tpo .deps/CXXSpace.Plo mv -f .deps/CXXQADSurfaceStaticData.Tpo .deps/CXXQADSurfaceStaticData.Plo mv -f .deps/CXXNewHood.Tpo .deps/CXXNewHood.Plo mv -f .deps/CXXSurface.Tpo .deps/CXXSurface.Plo mv -f .deps/CXXBall.Tpo .deps/CXXBall.Plo mv -f .deps/CXXQADSurface.Tpo .deps/CXXQADSurface.Plo mv -f .deps/CXXUtils.Tpo .deps/CXXUtils.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O -Wall -Wno-unused -o libcoot-electrostatics.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-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-pre-release-gtk2-python/lib -lrfftw -lfftw -L/d/emsley/autobuild/install-pre-release-gtk2-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/surface' Making all in coot-surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-surface' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -o rgbreps.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -I/d/emsley/autobuild/install-pre-release-gtk2-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 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-pre-release-gtk2-python/lib coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -L/d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/lib -lmmdb2 -L/d/emsley/autobuild/install-pre-release-gtk2-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-surface' Making all in lidia-core make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lidia-core' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-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++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c -o lig-build.lo lig-build.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT rdkit-interface.lo -MD -MP -MF .deps/rdkit-interface.Tpo -c -o rdkit-interface.lo rdkit-interface.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT cod-types.lo -MD -MP -MF .deps/cod-types.Tpo -c -o cod-types.lo cod-types.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT bond-record-container-t.lo -MD -MP -MF .deps/bond-record-container-t.Tpo -c -o bond-record-container-t.lo bond-record-container-t.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT cod-atom-type-t.lo -MD -MP -MF .deps/cod-atom-type-t.Tpo -c -o cod-atom-type-t.lo cod-atom-type-t.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 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-I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c lbg-molfile.cc -o lbg-molfile.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE 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-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT cod-atom-type-t.lo -MD -MP -MF .deps/cod-atom-type-t.Tpo -c cod-atom-type-t.cc -o cod-atom-type-t.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT atom-types.lo -MD -MP -MF .deps/atom-types.Tpo -c -o atom-types.lo atom-types.cc mv -f .deps/bond-record-container-t.Tpo .deps/bond-record-container-t.Plo libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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 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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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lidia-core' Making all in coords make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coords' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" 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cos-sin.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -g -O -Wall -Wno-unused -MT mmdb-extras.lo -MD -MP 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-DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -g -O -Wall -Wno-unused -MT mmdb.lo -MD -MP -MF .deps/mmdb.Tpo -c -o mmdb.lo mmdb.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include 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-I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -g -O -Wall -Wno-unused -MT Bond_lines_ext.lo -MD -MP -MF .deps/Bond_lines_ext.Tpo -c -o Bond_lines_ext.lo Bond_lines_ext.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 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-I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-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 libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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 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--mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-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 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -g -O -Wall -Wno-unused -MT loop-path.lo -MD -MP -MF .deps/loop-path.Tpo -c -o loop-path.lo loop-path.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/include/boost-0 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DPKGDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share/coot\" -DDATADIR=\"/d/emsley/autobuild/install-pre-release-gtk2-python/share\" -g -O -Wall -Wno-unused -MT loop-path.lo -MD -MP -MF .deps/loop-path.Tpo -c loop-path.cc -o loop-path.o mv -f .deps/phenix-geo.Tpo .deps/phenix-geo.Plo mv -f .deps/Bond_lines_ext.Tpo .deps/Bond_lines_ext.Plo mv -f .deps/loop-path.Tpo .deps/loop-path.Plo mv -f .deps/mmdb-crystal.Tpo .deps/mmdb-crystal.Plo mv -f .deps/phenix-geo-bonds.Tpo .deps/phenix-geo-bonds.Plo mv -f .deps/mmdb.Tpo .deps/mmdb.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-pre-release-gtk2-python/share/coot"' -DDATADIR='"/d/emsley/autobuild/install-pre-release-gtk2-python/share"' -g -O -Wall -Wno-unused -o libcoot-coords.la -rpath /d/emsley/autobuild/install-pre-release-gtk2-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 loop-path.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -L/d/emsley/autobuild/install-pre-release-gtk2-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 loop-path.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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coords' Making all in angles make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/angles' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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 AngleInfo.cc -o libcoot_AngleInfo_la-AngleInfo.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/angles' Making all in skeleton make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/skeleton' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c -o dm-utils.lo dm-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c -o BuildCas.lo BuildCas.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -o BuildCas.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I.. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/d/emsley/autobuild/install-pre-release-gtk2-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 /d/emsley/autobuild/install-pre-release-gtk2-python/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -L/d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/lib -lmmdb2 libtool: link: ar cru .libs/libcoot-skeleton.a dm-utils.o graphical_skel.o BuildCas.o libtool: link: ranlib .libs/libcoot-skeleton.a libtool: link: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" ) make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/skeleton' Making all in ccp4mg-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ccp4mg-utils' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c -o geomutil.lo geomutil.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c -o cartesian.lo cartesian.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" -DPACKAGE_STRING=\"coot\ 0.8.9.3-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-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=\"0.8.9.3-pre\" "-DPACKAGE_STRING=\"coot 0.8.9.3-pre\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.9.3-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_PYTHON=\"2.7\" -I. -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DUSE_LIBPNG -I/d/emsley/autobuild/install-pre-release-gtk2-python/include -g -O -Wall -Wno-unused -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o mv -f .deps/quat.Tpo .deps/quat.Plo mv -f .deps/cartesian.Tpo .deps/cartesian.Plo mv -f .deps/geomutil.Tpo .deps/geomutil.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_2020-01-02__T17_04_58/coot-0.8.9.3-pre' 1 --------------------------------------------------------------- make install 1 ---------------------------------------------------------------- Making install in auxil make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' Making install in catcheck make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/catcheck' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/catcheck' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/catcheck' Making install in rama make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/rama' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/rama' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/rama' Making install in sec-str make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/sec-str' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/sec-str' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/sec-str' Making install in strand-analysis make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/strand-analysis' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/strand-analysis' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/strand-analysis' Making install in vectors make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/vectors' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/vectors' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil/vectors' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/auxil' Making install in scheme make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/scheme' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/scheme' make[2]: Nothing to be done for `install-exec-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-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 add-linked-cho.scm find-baddies.scm '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/scheme' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/scheme' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/scheme' Making install in python make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python' make[2]: Nothing to be done for `install-exec-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/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-pre-release-gtk2-python/lib/python2.7/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 add_linked_cho.py find_baddies.py pdbe_validation_data.py ligand_validation_sliders.py chemical_feature_clusters.py res_spec_utils.py coot_output_to_window.py '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages/coot' Byte-compiling python modules... coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycho_restraints_from_models.pyinteractive_nudge_residues.pyacedrg_link.pycoot_toolbuttons.pyrcrane_loader.pyadd_linked_cho.pyfind_baddies.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.pycoot_output_to_window.py Byte-compiling python modules (optimized versions) ... coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycho_restraints_from_models.pyinteractive_nudge_residues.pyacedrg_link.pycoot_toolbuttons.pyrcrane_loader.pyadd_linked_cho.pyfind_baddies.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.pycoot_output_to_window.py make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python' Making install in pdb-templates make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pdb-templates' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pdb-templates' make[2]: Nothing to be done for `install-exec-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-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-NAG-core-NAG-SER.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-pre-release-gtk2-python/share/coot' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pdb-templates' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pdb-templates' Making install in macros make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/macros' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/macros' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/macros' Making install in compat make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/compat' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/compat' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/compat' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-compat.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 coot-getopt.h coot-sysdep.h getopt_int.h sleep-fixups.h '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/compat' libtool: install: /usr/bin/install -c .libs/libcoot-compat.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-compat.la libtool: install: /usr/bin/install -c .libs/libcoot-compat.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-compat.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-compat.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-compat.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/compat' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/compat' Making install in utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/utils' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-utils.la '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/include/coot/utils' libtool: install: /usr/bin/install -c .libs/libcoot-utils.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-utils.la libtool: install: /usr/bin/install -c .libs/libcoot-utils.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-utils.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-utils.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-utils.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/utils' Making install in protein_db make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/protein_db' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/protein_db' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/protein_db' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/protein_db' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-protein-db.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 protein_db.h protein_db_utils.h rna_db.h '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/protein_db' /usr/bin/install -c -m 644 protein.db '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/protein_db' libtool: install: /usr/bin/install -c .libs/libcoot-protein-db.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-protein-db.la libtool: install: /usr/bin/install -c .libs/libcoot-protein-db.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-protein-db.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-protein-db.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-protein-db.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/protein_db' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/protein_db' Making install in mini-mol make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/mini-mol' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-mini-mol.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 mini-mol.hh mini-mol-utils.hh atom-quads.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/mini-mol' libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-mini-mol.la libtool: install: /usr/bin/install -c .libs/libcoot-mini-mol.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-mini-mol.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-mini-mol.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-mini-mol.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/mini-mol' Making install in geometry make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/geometry' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/geometry' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/geometry' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-geometry.la '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/include/coot/geometry' libtool: install: /usr/bin/install -c .libs/libcoot-geometry.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-geometry.la libtool: install: /usr/bin/install -c .libs/libcoot-geometry.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-geometry.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-geometry.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-geometry.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/bin' libtool: install: /usr/bin/install -c coot-compare-dictionaries //d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot-compare-dictionaries libtool: install: /usr/bin/install -c coot-make-shelx-restraints //d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot-make-shelx-restraints libtool: install: /usr/bin/install -c coot-available-comp-id //d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot-available-comp-id make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/geometry' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/geometry' Making install in coot-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-utils' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-utils' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-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-pre-release-gtk2-python/include/coot/coot-utils' libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-utils.la libtool: install: /usr/bin/install -c .libs/libcoot-shelx.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-shelx.la libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-extras.la libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-utils.la libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-heavy.la libtool: install: /usr/bin/install -c .libs/libcoot-coord-utils.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-utils.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-utils.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-utils.a libtool: install: /usr/bin/install -c .libs/libcoot-shelx.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-shelx.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-shelx.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-shelx.a libtool: install: /usr/bin/install -c .libs/libcoot-coord-extras.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-extras.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-extras.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coord-extras.a libtool: install: /usr/bin/install -c .libs/libcoot-map-utils.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-utils.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-utils.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-utils.a libtool: install: /usr/bin/install -c .libs/libcoot-map-heavy.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-heavy.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-heavy.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-map-heavy.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-utils' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-utils' Making install in surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/surface' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/surface' make[2]: Nothing to be done for `install-data-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-electrostatics.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-electrostatics.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-electrostatics.la libtool: install: /usr/bin/install -c .libs/libcoot-electrostatics.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-electrostatics.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-electrostatics.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-electrostatics.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/surface' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/surface' Making install in coot-surface make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-surface' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-surface' make[2]: Nothing to be done for `install-data-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-surface.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-surface.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-surface.la libtool: install: /usr/bin/install -c .libs/libcoot-surface.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-surface.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-surface.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-surface.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-surface' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coot-surface' Making install in lidia-core make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lidia-core' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lidia-core' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/lidia-core' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-lidia-core.la '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/include/coot/lidia-core' libtool: install: /usr/bin/install -c .libs/libcoot-lidia-core.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia-core.la libtool: install: /usr/bin/install -c .libs/libcoot-lidia-core.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia-core.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia-core.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia-core.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lidia-core' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lidia-core' Making install in coords make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coords' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coords' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/coords' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-coords.la '//d/emsley/autobuild/install-pre-release-gtk2-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 loop-path.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/coords' libtool: install: /usr/bin/install -c .libs/libcoot-coords.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coords.la libtool: install: /usr/bin/install -c .libs/libcoot-coords.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coords.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coords.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-coords.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coords' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/coords' Making install in angles make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/angles' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/angles' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/angles' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-AngleInfo.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 AngleInfo.h ncube.h wrapped-ncube.h '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/angles' libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-AngleInfo.la libtool: install: /usr/bin/install -c .libs/libcoot-AngleInfo.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-AngleInfo.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-AngleInfo.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-AngleInfo.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/angles' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/angles' Making install in skeleton make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/skeleton' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/skeleton' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/skeleton' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-skeleton.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 graphical_skel.h dm-utils.h BuildCas.h '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/skeleton' libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-skeleton.la libtool: install: /usr/bin/install -c .libs/libcoot-skeleton.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-skeleton.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-skeleton.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-skeleton.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/skeleton' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/skeleton' Making install in ccp4mg-utils make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ccp4mg-utils' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ccp4mg-utils' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/ccp4mg-utils' /bin/sh ../libtool --mode=install /usr/bin/install -c libccp4mg-utils.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 geomutil.h mgtree.h cartesian.h matrix.h quat.h ppmutil.h '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/ccp4mg-utils' libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4mg-utils.la libtool: install: /usr/bin/install -c .libs/libccp4mg-utils.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4mg-utils.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4mg-utils.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libccp4mg-utils.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ccp4mg-utils' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ccp4mg-utils' Making install in density-contour make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/density-contour' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/density-contour' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/density-contour' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-isosurface.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 Vectors.h CIsoSurface.h density-contour-triangles.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/density-contour' libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-isosurface.la libtool: install: /usr/bin/install -c .libs/libcoot-isosurface.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-isosurface.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-isosurface.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-isosurface.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/density-contour' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/density-contour' Making install in db-main make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/db-main' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/db-main' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/db-main' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-db-main.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 db-main.hh db-strands.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/db-main' libtool: install: /usr/bin/install -c .libs/libcoot-db-main.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-db-main.la libtool: install: /usr/bin/install -c .libs/libcoot-db-main.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-db-main.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-db-main.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-db-main.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/db-main' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/db-main' Making install in analysis make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/analysis' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/analysis' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/analysis' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-analysis.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 bfkurt.hh mogul-interface.hh stats.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/analysis' libtool: install: /usr/bin/install -c .libs/libcoot-analysis.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-analysis.la libtool: install: /usr/bin/install -c .libs/libcoot-analysis.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-analysis.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-analysis.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-analysis.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c coot-bfactan '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' libtool: install: /usr/bin/install -c coot-bfactan //d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot-bfactan make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/analysis' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/analysis' Making install in ideal make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ideal' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ideal' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/libexec' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/ideal' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-ideal.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c coot-mini-rsr '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /usr/bin/install -c -m 644 test-indexing.hh simple-restraint.hh pepflip.hh regularize-minimol.hh lograma.h zo-rama.hh phi-psi.hh parallel-planes.hh torsion-bonds.hh extra-restraints.hh model-bond-deltas.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/ideal' /bin/sh ../libtool --mode=install /usr/bin/install -c mini-rsr-bin '//d/emsley/autobuild/install-pre-release-gtk2-python/libexec' libtool: install: /usr/bin/install -c .libs/libcoot-ideal.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ideal.la libtool: install: /usr/bin/install -c mini-rsr-bin //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/mini-rsr-bin libtool: install: /usr/bin/install -c .libs/libcoot-ideal.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ideal.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ideal.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ideal.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ideal' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ideal' Making install in ligand make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ligand' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ligand' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/libexec' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/ligand' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/data' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-ligand.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c findwaters findligand '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /usr/bin/install -c -m 644 ligands-2016.db '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/data' /bin/sh ../libtool --mode=install /usr/bin/install -c findligand-bin findwaters-bin coot-make-ligands-db '//d/emsley/autobuild/install-pre-release-gtk2-python/libexec' /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-pre-release-gtk2-python/include/coot/ligand' libtool: install: /usr/bin/install -c .libs/libcoot-ligand.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ligand.la libtool: install: /usr/bin/install -c .libs/libcoot-ligand.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ligand.a libtool: install: /usr/bin/install -c findligand-bin //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/findligand-bin libtool: install: /usr/bin/install -c findwaters-bin //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/findwaters-bin libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ligand.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-ligand.a libtool: install: /usr/bin/install -c coot-make-ligands-db //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/coot-make-ligands-db libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ligand' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/ligand' Making install in high-res make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/high-res' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/high-res' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/high-res' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-high-res.la '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/include/coot/high-res' libtool: install: /usr/bin/install -c .libs/libcoot-high-res.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-high-res.la libtool: install: /usr/bin/install -c .libs/libcoot-high-res.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-high-res.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-high-res.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-high-res.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/high-res' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/high-res' Making install in build make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/build' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/build' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/build' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-cabuild.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 CalphaBuild.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/build' libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-cabuild.la libtool: install: /usr/bin/install -c .libs/libcoot-cabuild.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-cabuild.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-cabuild.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-cabuild.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/build' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/build' Making install in greg-tests make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/greg-tests' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/greg-tests' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/greg-tests' Making install in python-tests make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python-tests' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-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_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python-tests' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/python-tests' Making install in tw make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/tw' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/tw' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/tw' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-tw.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 coot-tw.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/tw' libtool: install: /usr/bin/install -c .libs/libcoot-tw.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-tw.la libtool: install: /usr/bin/install -c .libs/libcoot-tw.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-tw.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-tw.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-tw.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/tw' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/tw' Making install in libgtkgraph make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/libgtkgraph' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/libgtkgraph' make[2]: Nothing to be done for `install-data-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-gtkgraph.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-gtkgraph.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-gtkgraph.la libtool: install: /usr/bin/install -c .libs/libcoot-gtkgraph.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-gtkgraph.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-gtkgraph.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-gtkgraph.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/libgtkgraph' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/libgtkgraph' Making install in lbg make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lbg' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lbg' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot/pixmaps' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-lidia.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages/lidia' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-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-pre-release-gtk2-python/share/coot/pixmaps' /usr/bin/install -c -m 644 lbg.glade lbg-callbacks.cc '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' /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-pre-release-gtk2-python/include/coot/lbg' /usr/bin/install -c -m 644 __init__.py fetch.py '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages/lidia' libtool: install: /usr/bin/install -c .libs/libcoot-lidia.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia.la libtool: install: /usr/bin/install -c .libs/libcoot-lidia.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia.a Byte-compiling python modules... __init__.pyfetch.py libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-lidia.a Byte-compiling python modules (optimized versions) ... __init__.pyfetch.py libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c lidia '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' libtool: install: /usr/bin/install -c lidia //d/emsley/autobuild/install-pre-release-gtk2-python/bin/lidia make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lbg' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/lbg' Making install in cootaneer make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootaneer' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootaneer' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' /bin/sh ../libtool --mode=install /usr/bin/install -c libcootaneer.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 cootaneer-llk-2.40.dat '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' libtool: install: /usr/bin/install -c .libs/libcootaneer.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootaneer.la libtool: install: /usr/bin/install -c .libs/libcootaneer.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootaneer.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootaneer.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootaneer.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootaneer' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootaneer' Making install in cootilus make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootilus' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootilus' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcootilus.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 nautilus_lib.pdb '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' libtool: install: /usr/bin/install -c .libs/libcootilus.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootilus.la libtool: install: /usr/bin/install -c .libs/libcootilus.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootilus.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootilus.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcootilus.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootilus' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/cootilus' Making install in goograph make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/goograph' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/goograph' make[2]: Nothing to be done for `install-data-am'. /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-goograph.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' libtool: install: /usr/bin/install -c .libs/libcoot-goograph.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-goograph.la libtool: install: /usr/bin/install -c .libs/libcoot-goograph.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-goograph.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-goograph.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-goograph.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/goograph' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/goograph' Making install in pli make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pli' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pli' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/pli' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libcoot-pli.la '//d/emsley/autobuild/install-pre-release-gtk2-python/lib' /usr/bin/install -c -m 644 flev-annotations.hh protein-ligand-interactions.hh pi-stacking.hh specs.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot/pli' libtool: install: /usr/bin/install -c .libs/libcoot-pli.lai //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-pli.la libtool: install: /usr/bin/install -c .libs/libcoot-pli.a //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-pli.a libtool: install: chmod 644 //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-pli.a libtool: install: ranlib //d/emsley/autobuild/install-pre-release-gtk2-python/lib/libcoot-pli.a libtool: install: warning: remember to run `libtool --finish /d/emsley/autobuild/install-pre-release-gtk2-python/lib' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pli' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pli' Making install in pyrogen make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pyrogen' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pyrogen' make install-exec-hook make[3]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pyrogen' make[3]: Nothing to be done for `install-exec-hook'. make[3]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pyrogen' make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pyrogen' make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/pyrogen' Making install in src make[1]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/src' make[2]: Entering directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/src' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /usr/bin/install -c coot coot-density-score-by-residue dynarama '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c coot-fix-nomenclature-errors '//d/emsley/autobuild/install-pre-release-gtk2-python/bin' libtool: install: /usr/bin/install -c coot-fix-nomenclature-errors //d/emsley/autobuild/install-pre-release-gtk2-python/bin/coot-fix-nomenclature-errors /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/libexec' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages' /usr/bin/mkdir -p '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages' /bin/sh ../libtool --mode=install /usr/bin/install -c coot-bin coot-density-score-by-residue-bin dynarama-bin '//d/emsley/autobuild/install-pre-release-gtk2-python/libexec' /usr/bin/install -c -m 644 crunch-model.hh '//d/emsley/autobuild/install-pre-release-gtk2-python/include/coot' /usr/bin/install -c -m 644 dynarama.glade '//d/emsley/autobuild/install-pre-release-gtk2-python/share/coot' /usr/bin/install -c coot.py coot.pth '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages' /usr/bin/install -c -m 644 coot.py coot.pth '//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages' libtool: install: /usr/bin/install -c coot-bin //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/coot-bin Byte-compiling python modules... coot.py/usr/bin/install: cannot create regular file ‘//d/emsley/autobuild/install-pre-release-gtk2-python/lib/python2.7/site-packages/coot.pth’: File exists make[2]: *** [install-dist_pythonSCRIPTS] Error 1 make[2]: *** Waiting for unfinished jobs.... Byte-compiling python modules (optimized versions) ... coot.py libtool: install: /usr/bin/install -c coot-density-score-by-residue-bin //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/coot-density-score-by-residue-bin libtool: install: /usr/bin/install -c dynarama-bin //d/emsley/autobuild/install-pre-release-gtk2-python/libexec/dynarama-bin make[2]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/src' make[1]: *** [install-am] Error 2 make[1]: Leaving directory `/d/emsley/autobuild/building/charybdis_2020-01-02__T17_04_58/coot-0.8.9.3-pre/src' make: *** [install-recursive] Error 1