* Package: sci-chemistry/coot-0.6.2 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: amd64 elibc_glibc kernel_linux multilib openmp userland_GNU * FEATURES: sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking coot-0.6.2.tar.gz to /tmp/portage/sci-chemistry/coot-0.6.2/work >>> Source unpacked in /tmp/portage/sci-chemistry/coot-0.6.2/work >>> Preparing source in /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2 ... * Applying 0.6.2-clipper-config.patch ... [ ok ] * Applying 0.6.2-mmdb-config.patch ... [ ok ] * Applying 0.6.2-gl.patch ... [ ok ] * Applying 0.6.2-test.patch ... [ ok ] * Applying 0.6.2-ssm.patch ... [ ok ] * Applying 0.6.2-libpng15.patch ... [ ok ] * Running eautoreconf in '/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2' ... * Running aclocal -I macros ... [ ok ] * Running libtoolize --copy --force --install --automake ... [ ok ] * Running aclocal -I macros ... [ ok ] * Running autoconf ... [ ok ] * Running automake --add-missing --copy ... [ ok ] * Running elibtoolize in: coot-0.6.2/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.2.6 patch ... >>> Source prepared. >>> Configuring source in /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2 ... * econf: updating coot-0.6.2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating coot-0.6.2/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --includedir=${prefix}/include/coot --with-gtkcanvas-prefix=/usr --with-gtkgl-prefix=/usr --with-guile --with-python=/usr --with-guile-gtk --with-gtk2 --with-pygtk --enable-openmp checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 checking for library containing strerror... none required checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) gcc3 checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) gcc3 checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... gcc3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/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-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... no checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/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 sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp checking if this is MINGW on Windows... no checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for x86_64-pc-linux-gnu-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... 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 GLUT... yes checking for MMDB... yes checking for MMDB... yes checking for MMDBSSM... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile... /usr/bin/guile checking for guile-config... /usr/bin/guile-config checking for guile-tools... /usr/bin/guile-tools checking libguile compile flags... -pthread checking libguile link flags... -pthread -L/usr/lib64 -lguile -lltdl -lgmp -lcrypt -lm -lltdl checking for Guile-Lib... yes checking for guile-gui... yes checking GUILE_VERSION: 1.8 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 guile-gtk... checking libglade... yes Not using database checking for curl >= 7.9.7... 7.21.4 checking build type... which: no rpm in (/usr/lib64/portage/bin/ebuild-helpers:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.5.3) Linux-GenuineIntel---python-gtk2 configure: creating ./config.status config.status: creating Makefile config.status: creating macros/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 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 greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating lidia-core/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 rama-data/Makefile 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: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2 ... make -j4 Making all in auxil make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil' Making all in catcheck make[2]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/catcheck' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/catcheck' Making all in rama make[2]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/rama' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/rama' Making all in sec-str make[2]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/sec-str' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/strand-analysis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/strand-analysis' Making all in vectors make[2]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/vectors' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/vectors' make[2]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil' make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil' Making all in scheme make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/scheme' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/scheme' Making all in python make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/python' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/python' Making all in macros make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/macros' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/macros' Making all in compat make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/compat' /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -march=native -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -march=native -O2 -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c -o getopt1.lo getopt1.c libtool: compile: x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -march=native -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -fPIC -DPIC -o .libs/getopt.o libtool: compile: x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -march=native -O2 -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -fPIC -DPIC -o .libs/getopt1.o libtool: compile: x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -march=native -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -march=native -O2 -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o >/dev/null 2>&1 mv -f .deps/getopt.Tpo .deps/getopt.Plo mv -f .deps/getopt1.Tpo .deps/getopt1.Plo /bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-compat.la -rpath /usr/lib64 getopt.lo getopt1.lo libtool: link: x86_64-pc-linux-gnu-gcc -shared -fPIC -DPIC .libs/getopt.o .libs/getopt1.o -Wl,--as-needed -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-compat.so.0 -o .libs/libcoot-compat.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-compat.so.0" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-compat.so" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-compat.a getopt.o getopt1.o libtool: link: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/compat' Making all in utils make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 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-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c coot-fasta.cc -fPIC -DPIC -o .libs/coot-fasta.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -fPIC -DPIC -o .libs/coot-utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c gdk-keysyms.cc -fPIC -DPIC -o .libs/gdk-keysyms.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c coot-fasta.cc -o coot-fasta.o >/dev/null 2>&1 mv -f .deps/coot-fasta.Tpo .deps/coot-fasta.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c atomic-numbers.cc -o atomic-numbers.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -o coot-utils.o >/dev/null 2>&1 mv -f .deps/atomic-numbers.Tpo .deps/atomic-numbers.Plo mv -f .deps/coot-utils.Tpo .deps/coot-utils.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 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-Wl,--as-needed -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-utils.so.0 -o .libs/libcoot-utils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-utils.so.0" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-utils.so" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-utils.a coot-utils.o coot-fasta.o atomic-numbers.o gdk-keysyms.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-utils.a libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln 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-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c energy-lib.cc -fPIC -DPIC -o .libs/energy-lib.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -o protein-geometry-mmdb.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c read-sbase.cc -o read-sbase.o >/dev/null 2>&1 mv -f .deps/protein-geometry-mmdb.Tpo .deps/protein-geometry-mmdb.Plo x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -MT test-geometry.o -MD -MP -MF .deps/test-geometry.Tpo -c -o test-geometry.o test-geometry.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c energy-lib.cc -o energy-lib.o >/dev/null 2>&1 mv -f .deps/read-sbase.Tpo .deps/read-sbase.Plo x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -MT test-read-components.o -MD -MP -MF .deps/test-read-components.Tpo -c -o test-read-components.o test-read-components.cc mv -f .deps/test-read-components.Tpo .deps/test-read-components.Po mv -f .deps/energy-lib.Tpo .deps/energy-lib.Plo mv -f .deps/test-geometry.Tpo .deps/test-geometry.Po libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -o protein-geometry.o >/dev/null 2>&1 mv -f .deps/protein-geometry.Tpo .deps/protein-geometry.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-geometry.la -rpath /usr/lib64 protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo ../utils/libcoot-utils.la -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../utils/.libs/libcoot-utils.so -L/usr/lib64 /usr/lib64/libclipper-minimol.so -L/usr/lib /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so.0" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-geometry.a protein-geometry.o protein-geometry-mmdb.o read-sbase.o energy-lib.o libtool: link: x86_64-pc-linux-gnu-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 x86_64-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-geometry test-geometry.o ./libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-read-components test-read-components.o ./libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/test-geometry test-geometry.o -Wl,--as-needed ./.libs/libcoot-geometry.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/test-read-components test-read-components.o -Wl,--as-needed ./.libs/libcoot-geometry.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry' Making all in mini-mol make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c -o atom-quads.lo atom-quads.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT testminimol.o -MD -MP -MF .deps/testminimol.Tpo -c -o testminimol.o testminimol.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -fPIC -DPIC -o .libs/atom-quads.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -fPIC -DPIC -o .libs/mini-mol.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -fPIC -DPIC -o .libs/mini-mol-utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -o atom-quads.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -o mini-mol-utils.o >/dev/null 2>&1 mv -f .deps/testminimol.Tpo .deps/testminimol.Po mv -f .deps/atom-quads.Tpo .deps/atom-quads.Plo mv -f .deps/mini-mol-utils.Tpo .deps/mini-mol-utils.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -o mini-mol.o >/dev/null 2>&1 mv -f .deps/mini-mol.Tpo .deps/mini-mol.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-mini-mol.la -rpath /usr/lib64 mini-mol.lo mini-mol-utils.lo atom-quads.lo -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o -Wl,--as-needed -L/usr/lib64 /usr/lib64/libclipper-minimol.so -L/usr/lib /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so.0" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-mini-mol.a mini-mol.o mini-mol-utils.o atom-quads.o libtool: link: x86_64-pc-linux-gnu-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" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o testminimol testminimol.o libcoot-mini-mol.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/testminimol testminimol.o -Wl,--as-needed ./.libs/libcoot-mini-mol.so -L/usr/lib64 -L/usr/lib /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol' Making all in coot-utils make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 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2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT coot-h-bonds.lo -MD -MP -MF .deps/coot-h-bonds.Tpo -c coot-h-bonds.cc -o coot-h-bonds.o >/dev/null 2>&1 mv -f .deps/coot-coord-utils-nucleotides.Tpo .deps/coot-coord-utils-nucleotides.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" 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/usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm ../utils/.libs/libcoot-utils.so libtool: link: x86_64-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/testcootutils test-utils.o -Wl,--as-needed ./.libs/libcoot-shelx.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ./.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm ../utils/.libs/libcoot-utils.so mv -f .deps/coot-fffear.Tpo .deps/coot-fffear.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-map-heavy.la -rpath /usr/lib64 coot-map-heavy.lo coot-fffear.lo ../mini-mol/libcoot-mini-mol.la libcoot-map-utils.la libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib64 -lgsl -lgslcblas -lm libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/coot-map-heavy.o .libs/coot-fffear.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib64 -L/usr/lib ./.libs/libcoot-map-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ./.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb ../utils/.libs/libcoot-utils.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-map-heavy.so.0" && ln -s "libcoot-map-heavy.so.0.0.0" "libcoot-map-heavy.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-map-heavy.so" && ln -s "libcoot-map-heavy.so.0.0.0" "libcoot-map-heavy.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-map-heavy.a coot-map-heavy.o coot-fffear.o libtool: link: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils' Making all in surface make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 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-I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c CXXCircle.cpp -o CXXCircle.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -o CXXChargeTable.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" 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-I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXBall.lo -MD -MP -MF .deps/CXXBall.Tpo -c CXXBall.cpp -o CXXBall.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 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-DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -o CXXQADSurfaceStaticData.o >/dev/null 2>&1 mv -f .deps/CXXSurface.Tpo .deps/CXXSurface.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c -o CXXSpace.lo CXXSpace.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -fPIC -DPIC -o .libs/CXXSpace.o mv -f .deps/CXXQADSurfaceStaticData.Tpo .deps/CXXQADSurfaceStaticData.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c -o CXXUtils.lo CXXUtils.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c CXXUtils.cpp -fPIC -DPIC -o .libs/CXXUtils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -o CXXSpace.o >/dev/null 2>&1 mv -f .deps/CXXSpace.Tpo .deps/CXXSpace.Plo mv -f .deps/CXXBall.Tpo .deps/CXXBall.Plo mv -f .deps/CXXQADSurface.Tpo .deps/CXXQADSurface.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -march=native -O2 -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c CXXUtils.cpp -o CXXUtils.o >/dev/null 2>&1 mv -f .deps/CXXUtils.Tpo .deps/CXXUtils.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libccp4mg-surface.la -rpath /usr/lib64 CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXBall.lo CXXQADSurfaceStaticData.lo CXXSpace.lo CXXUtils.lo -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXBall.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o .libs/CXXUtils.o -Wl,--as-needed -L/usr/lib64 /usr/lib64/libclipper-minimol.so -L/usr/lib /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libccp4mg-surface.so.0 -o .libs/libccp4mg-surface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so.0" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so.0") libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libccp4mg-surface.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: x86_64-pc-linux-gnu-ranlib .libs/libccp4mg-surface.a libtool: link: ( cd ".libs" && rm -f "libccp4mg-surface.la" && ln -s "../libccp4mg-surface.la" "libccp4mg-surface.la" ) make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface' Making all in coot-surface make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-surface' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c -o rgbreps.lo rgbreps.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -fPIC -DPIC -o .libs/coot-surface.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -fPIC -DPIC -o .libs/rgbreps.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -o rgbreps.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -o coot-surface.o >/dev/null 2>&1 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 x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-surface.la -rpath /usr/lib64 coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lglut -lXmu -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb -lGL libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs -Wl,--as-needed ../surface/.libs/libccp4mg-surface.so -L/usr/lib64 -L/usr/lib -lglut -lXmu /usr/lib64/libgtk-x11-2.0.so /usr/lib64/libgdk-x11-2.0.so /usr/lib64/libatk-1.0.so -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpng14 -lpango-1.0 /usr/lib64/libfontconfig.so -lfreetype -lz -lbz2 -lexpat -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -lGL -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -pthread -pthread -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-surface.so.0" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-surface.so" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-surface.a coot-surface.o rgbreps.o libtool: link: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-surface' Making all in lidia-core make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -march=native -O2 -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c -o lig-build.lo lig-build.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -march=native -O2 -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c lig-build.cc -fPIC -DPIC -o .libs/lig-build.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -march=native -O2 -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c lbg-molfile.cc -fPIC -DPIC -o .libs/lbg-molfile.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -march=native -O2 -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c lig-build.cc -o lig-build.o >/dev/null 2>&1 mv -f .deps/lig-build.Tpo .deps/lig-build.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -march=native -O2 -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c lbg-molfile.cc -o lbg-molfile.o >/dev/null 2>&1 mv -f .deps/lbg-molfile.Tpo .deps/lbg-molfile.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-lidia-core.la -rpath /usr/lib64 lbg-molfile.lo lig-build.lo libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/lbg-molfile.o .libs/lig-build.o -Wl,--as-needed -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-lidia-core.so.0" && ln -s "libcoot-lidia-core.so.0.0.0" "libcoot-lidia-core.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-lidia-core.so" && ln -s "libcoot-lidia-core.so.0.0.0" "libcoot-lidia-core.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-lidia-core.a lbg-molfile.o lig-build.o libtool: link: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core' Making all in coords make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c -o Bond_lines.lo Bond_lines.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -MT Cartesian.lo -MD -MP -MF .deps/Cartesian.Tpo -c -o Cartesian.lo Cartesian.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -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: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT Bond_lines_ext.lo -MD -MP -MF .deps/Bond_lines_ext.Tpo -c Bond_lines_ext.cc -fPIC -DPIC -o .libs/Bond_lines_ext.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc -o Bond_lines.o 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-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT coot-close.lo -MD -MP -MF .deps/coot-close.Tpo -c coot-close.cc -fPIC -DPIC -o .libs/coot-close.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT Bond_lines_ext.lo -MD -MP -MF .deps/Bond_lines_ext.Tpo -c Bond_lines_ext.cc -o Bond_lines_ext.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT coot-close.lo -MD -MP -MF .deps/coot-close.Tpo -c coot-close.cc -o coot-close.o >/dev/null 2>&1 mv -f .deps/coot-close.Tpo .deps/coot-close.Plo mv -f .deps/Bond_lines_ext.Tpo .deps/Bond_lines_ext.Plo mv -f .deps/Bond_lines.Tpo .deps/Bond_lines.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-coords.la -rpath /usr/lib64 Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../lidia-core/libcoot-lidia-core.la ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../lidia-core/.libs/libcoot-lidia-core.so ../geometry/.libs/libcoot-geometry.so -L/usr/lib64 -L/usr/lib ../coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-coords.so.0" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-coords.so" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so") libtool: link: x86_64-pc-linux-gnu-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 libtool: link: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords' Making all in angles make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -march=native -O2 -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 x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -march=native -O2 -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: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 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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/\" -I. -I/usr/include -I/usr/include -g -O1 -march=native -O2 -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 >/dev/null 2>&1 mv -f .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -march=native -O2 -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c AngleInfo.cc -o libcoot_AngleInfo_la-AngleInfo.o >/dev/null 2>&1 mv -f .deps/libcoot_AngleInfo_la-AngleInfo.Tpo .deps/libcoot_AngleInfo_la-AngleInfo.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -march=native -O2 -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF 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-L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -O1 -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-AngleInfo.so.0 -o .libs/libcoot-AngleInfo.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so.0" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so") libtool: link: x86_64-pc-linux-gnu-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: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles' Making all in skeleton make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/skeleton' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include 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-I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -fPIC -DPIC -o .libs/dm-utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -fPIC -DPIC -o .libs/graphical_skel.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -fPIC -DPIC -o .libs/BuildCas.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -o dm-utils.o >/dev/null 2>&1 mv -f .deps/dm-utils.Tpo .deps/dm-utils.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -o graphical_skel.o >/dev/null 2>&1 mv -f .deps/graphical_skel.Tpo .deps/graphical_skel.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -march=native -O2 -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -o BuildCas.o >/dev/null 2>&1 mv -f .deps/BuildCas.Tpo .deps/BuildCas.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-skeleton.la -rpath /usr/lib64 dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,--as-needed ../angles/.libs/libcoot-AngleInfo.so ../geometry/.libs/libcoot-geometry.so -L/usr/lib64 -L/usr/lib ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so 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-L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so.0" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-skeleton.a dm-utils.o graphical_skel.o BuildCas.o libtool: link: x86_64-pc-linux-gnu-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 `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/skeleton' Making all in ccp4mg-utils make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c -o geomutil.lo geomutil.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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cartesian.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -fPIC -DPIC -o .libs/cartesian.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -fPIC -DPIC -o .libs/matrix.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -fPIC -DPIC -o .libs/mgtree.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -fPIC -DPIC -o .libs/geomutil.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -o geomutil.o >/dev/null 2>&1 mv -f .deps/cartesian.Tpo .deps/cartesian.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c -o quat.lo quat.cc mv -f .deps/geomutil.Tpo .deps/geomutil.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c -o ppmutil.lo ppmutil.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -fPIC -DPIC -o .libs/quat.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -fPIC -DPIC -o .libs/ppmutil.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -o quat.o >/dev/null 2>&1 mv -f .deps/quat.Tpo .deps/quat.Plo mv -f .deps/matrix.Tpo .deps/matrix.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -o mgtree.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -march=native -O2 -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -o ppmutil.o >/dev/null 2>&1 mv -f .deps/ppmutil.Tpo .deps/ppmutil.Plo mv -f .deps/mgtree.Tpo .deps/mgtree.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libccp4mg-utils.la -rpath /usr/lib64 geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo -lpng libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/geomutil.o .libs/mgtree.o .libs/cartesian.o .libs/matrix.o .libs/quat.o .libs/ppmutil.o -Wl,--as-needed -lpng -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libccp4mg-utils.so.0 -o .libs/libccp4mg-utils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so.0" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so.0") libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libccp4mg-utils.a geomutil.o mgtree.o cartesian.o matrix.o quat.o ppmutil.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libccp4mg-utils.a libtool: link: ( cd ".libs" && rm -f "libccp4mg-utils.la" && ln -s "../libccp4mg-utils.la" "libccp4mg-utils.la" ) make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils' Making all in density-contour make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/density-contour' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c -o Vectors.lo Vectors.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c -o CIsoSurface.lo CIsoSurface.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT density-contour-triangles.lo -MD -MP -MF .deps/density-contour-triangles.Tpo -c -o density-contour-triangles.lo density-contour-triangles.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c CIsoSurface.cpp -fPIC -DPIC -o .libs/CIsoSurface.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT density-contour-triangles.lo -MD -MP -MF .deps/density-contour-triangles.Tpo -c density-contour-triangles.cc -fPIC -DPIC -o .libs/density-contour-triangles.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c Vectors.cpp -fPIC -DPIC -o .libs/Vectors.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c Vectors.cpp -o Vectors.o >/dev/null 2>&1 mv -f .deps/Vectors.Tpo .deps/Vectors.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT density-contour-triangles.lo -MD -MP -MF .deps/density-contour-triangles.Tpo -c density-contour-triangles.cc -o density-contour-triangles.o >/dev/null 2>&1 mv -f .deps/density-contour-triangles.Tpo .deps/density-contour-triangles.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -I/usr/include -march=native -O2 -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c CIsoSurface.cpp -o CIsoSurface.o >/dev/null 2>&1 mv -f .deps/CIsoSurface.Tpo .deps/CIsoSurface.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-isosurface.la -rpath /usr/lib64 Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,--as-needed ../coords/.libs/libcoot-coords.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so.0" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-isosurface.a Vectors.o CIsoSurface.o density-contour-triangles.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-isosurface.a libtool: link: ( cd ".libs" && rm -f "libcoot-isosurface.la" && ln -s "../libcoot-isosurface.la" "libcoot-isosurface.la" ) make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/density-contour' Making all in db-main make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c -o db-main.lo db-main.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c -o db-strands.lo db-strands.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -MT testdbmain.o -MD -MP -MF .deps/testdbmain.Tpo -c -o testdbmain.o testdbmain.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -MT train-pepflip.o -MD -MP -MF .deps/train-pepflip.Tpo -c -o train-pepflip.o train-pepflip.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -fPIC -DPIC -o .libs/db-strands.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -fPIC -DPIC -o .libs/db-main.o mv -f .deps/testdbmain.Tpo .deps/testdbmain.Po mv -f .deps/train-pepflip.Tpo .deps/train-pepflip.Po libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -o db-strands.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -o db-main.o >/dev/null 2>&1 mv -f .deps/db-strands.Tpo .deps/db-strands.Plo mv -f .deps/db-main.Tpo .deps/db-main.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-db-main.la -rpath /usr/lib64 db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/db-main.o .libs/db-strands.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib64 -L/usr/lib ../coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so.0" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-db-main.a db-main.o db-strands.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-db-main.a libtool: link: ( cd ".libs" && rm -f "libcoot-db-main.la" && ln -s "../libcoot-db-main.la" "libcoot-db-main.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o testdbmain testdbmain.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o train-pepflip train-pepflip.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/testdbmain testdbmain.o -Wl,--as-needed ./.libs/libcoot-db-main.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/train-pepflip train-pepflip.o -Wl,--as-needed ./.libs/libcoot-db-main.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main' Making all in ideal make[1]: Entering directory 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-DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../utils -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -march=native -O2 -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c simple-restraint.cc -o simple-restraint.o >/dev/null 2>&1 mv -f .deps/simple-restraint.Tpo .deps/simple-restraint.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -march=native -O2 -L/usr/lib64 -lgsl -lgslcblas -lm -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-ideal.la -rpath /usr/lib64 simple-restraint.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib64 -lgsl -lgslcblas -lm -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/simple-restraint.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/usr/lib64 -L/usr/lib -Wl,--as-needed ../geometry/.libs/libcoot-geometry.so ../coot-utils/.libs/libcoot-coord-extras.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-ideal.so.0" && ln -s "libcoot-ideal.so.0.0.0" "libcoot-ideal.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-ideal.so" && ln -s "libcoot-ideal.so.0.0.0" "libcoot-ideal.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-ideal.a simple-restraint.o extra-restraints.o pepflip.o regularize-minimol.o lograma.o extra-restraints-kk.o simple-restraint-kk.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-ideal.a libtool: link: ( cd ".libs" && rm -f "libcoot-ideal.la" && ln -s "../libcoot-ideal.la" "libcoot-ideal.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -march=native -O2 -L/usr/lib64 -lgsl -lgslcblas -lm -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o with-geometry with-geometry.o ./libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb -L/usr/lib64 -lgsl -lgslcblas -lm /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -march=native -O2 -L/usr/lib64 -lgsl -lgslcblas -lm -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o with-map with-map.o ./libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb -L/usr/lib64 -lgsl -lgslcblas -lm /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -march=native -O2 -L/usr/lib64 -lgsl -lgslcblas -lm -lmmdb -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o logramatest logramatest.o ./libcoot-ideal.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -L/usr/lib64 -lgsl -lgslcblas -lm libtool: link: x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/logramatest logramatest.o -L/usr/lib64 -L/usr/lib -Wl,--as-needed 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dunbrack.lo -MD -MP -MF .deps/dunbrack.Tpo -c dunbrack.cc -o dunbrack.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT chi-angles-autogen.lo -MD -MP -MF .deps/chi-angles-autogen.Tpo -c chi-angles-autogen.cc -o chi-angles-autogen.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT chi-angles.lo -MD -MP -MF .deps/chi-angles.Tpo -c chi-angles.cc -o chi-angles.o >/dev/null 2>&1 mv -f .deps/ligand.Tpo .deps/ligand.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" 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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/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT primitive-chi-angles.lo -MD -MP -MF .deps/primitive-chi-angles.Tpo -c primitive-chi-angles.cc -o primitive-chi-angles.o >/dev/null 2>&1 mv -f .deps/rotamer.Tpo .deps/rotamer.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 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-I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT dipole.lo -MD -MP -MF .deps/dipole.Tpo -c dipole.cc -o dipole.o >/dev/null 2>&1 mv -f .deps/base-pairing.Tpo .deps/base-pairing.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -MT backrub-rotamer.lo -MD -MP -MF .deps/backrub-rotamer.Tpo -c -o backrub-rotamer.lo backrub-rotamer.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT backrub-rotamer.lo -MD -MP -MF .deps/backrub-rotamer.Tpo -c backrub-rotamer.cc -fPIC -DPIC -o .libs/backrub-rotamer.o mv -f .deps/primitive-chi-angles.Tpo .deps/primitive-chi-angles.Plo x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -MT find-ligand.o -MD -MP -MF .deps/find-ligand.Tpo -c -o find-ligand.o find-ligand.cc mv -f .deps/rotamer-tables.Tpo .deps/rotamer-tables.Plo x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -MT find-waters.o -MD -MP -MF .deps/find-waters.Tpo -c -o find-waters.o find-waters.cc mv -f .deps/find-waters.Tpo .deps/find-waters.Po mv -f .deps/dipole.Tpo .deps/dipole.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../lidia-core -I../utils -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -MT backrub-rotamer.lo -MD -MP -MF .deps/backrub-rotamer.Tpo -c backrub-rotamer.cc -o backrub-rotamer.o >/dev/null 2>&1 mv -f .deps/find-ligand.Tpo .deps/find-ligand.Po mv -f .deps/backrub-rotamer.Tpo .deps/backrub-rotamer.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-ligand.la -rpath /usr/lib64 ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo ../ideal/libcoot-ideal.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../ideal/.libs/libcoot-ideal.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-extras.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-extras.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-ligand.a ligand.o ligand-extras.o residue_by_phi_psi.o wiggly-ligand.o monomer-utils.o dunbrack.o chi-angles-autogen.o chi-angles.o helix-placement.o fast-ss-search.o rigid-body.o ideal-rna.o richardson-rotamers.o richardson-rotamer.o rotamer.o torsion-general.o rotamer-tables.o primitive-chi-angles.o dipole.o base-pairing.o backrub-rotamer.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-ligand.a libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o findligand-real find-ligand.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb -L/usr/lib64 -lgsl -lgslcblas -lm /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o findwaters-real find-waters.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -L/usr/lib64 -lclipper-minimol 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../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../compat/.libs/libcoot-compat.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so -lm libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/findwaters-real find-waters.o -Wl,--as-needed ./.libs/libcoot-ligand.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs/libcoot-ideal.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs/libcoot-db-main.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs/libccp4mg-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-map-utils.so 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-I../utils -I../coot-utils -I../lidia-core -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DHAVE_GSL -I/usr/include -march=native -O2 -MT residue-distortions.lo -MD -MP -MF .deps/residue-distortions.Tpo -c residue-distortions.cc -o residue-distortions.o >/dev/null 2>&1 mv -f .deps/residue-distortions.Tpo .deps/residue-distortions.Plo libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DHAVE_GSL -I/usr/include -march=native -O2 -MT sequence-assignment.lo -MD -MP -MF .deps/sequence-assignment.Tpo -c sequence-assignment.cc -o sequence-assignment.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DHAVE_GSL -I/usr/include -march=native -O2 -MT coot-atom-graph.lo -MD -MP -MF .deps/coot-atom-graph.Tpo -c coot-atom-graph.cc -o coot-atom-graph.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../utils -I../coot-utils -I../lidia-core -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -DHAVE_GSL -I/usr/include -march=native -O2 -MT high-res.lo -MD -MP -MF .deps/high-res.Tpo -c high-res.cc -o high-res.o >/dev/null 2>&1 mv -f .deps/coot-atom-graph.Tpo .deps/coot-atom-graph.Plo mv -f .deps/sequence-assignment.Tpo .deps/sequence-assignment.Plo mv -f .deps/high-res.Tpo .deps/high-res.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-high-res.la -rpath /usr/lib64 high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ligand/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib64 -L/usr/lib ../ligand/.libs/libcoot-ligand.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs/libcoot-ideal.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs/libcoot-db-main.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs/libccp4mg-utils.so -lpng /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs/libcoot-coords.so 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/usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so.0" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-high-res.a high-res.o coot-atom-graph.o residue-distortions.o sequence-assignment.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-high-res.a libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" ) make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/high-res' Making all in build make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/build' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT CalphaBuild.lo -MD -MP -MF .deps/CalphaBuild.Tpo -c -o CalphaBuild.lo CalphaBuild.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT testcabuild.o -MD -MP -MF .deps/testcabuild.Tpo -c -o testcabuild.o testcabuild.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 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-MF .deps/CalphaBuild.Tpo -c CalphaBuild.cc -o CalphaBuild.o >/dev/null 2>&1 mv -f .deps/CalphaBuild.Tpo .deps/CalphaBuild.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-cabuild.la -rpath /usr/lib64 CalphaBuild.lo ../angles/libcoot-AngleInfo.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/CalphaBuild.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles/.libs -Wl,--as-needed ../angles/.libs/libcoot-AngleInfo.so -L/usr/lib64 /usr/lib64/libclipper-minimol.so -L/usr/lib /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so.0" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-cabuild.a CalphaBuild.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-cabuild.a libtool: link: ( cd ".libs" && rm -f "libcoot-cabuild.la" && ln -s "../libcoot-cabuild.la" "libcoot-cabuild.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o testcabuild testcabuild.o ./libcoot-cabuild.la ../angles/libcoot-AngleInfo.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/testcabuild testcabuild.o -Wl,--as-needed ./.libs/libcoot-cabuild.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/build' Making all in greg-tests make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/greg-tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/greg-tests' Making all in python-tests make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/python-tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/python-tests' Making all in analysis make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/analysis' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c -o bfkurt.lo bfkurt.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT bfactan.o -MD -MP -MF .deps/bfactan.Tpo -c -o bfactan.o bfactan.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -fPIC -DPIC -o .libs/bfkurt.o mv -f .deps/bfactan.Tpo .deps/bfactan.Po libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -o bfkurt.o >/dev/null 2>&1 mv -f .deps/bfkurt.Tpo .deps/bfkurt.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-analysis.la -rpath /usr/lib64 bfkurt.lo ../coot-utils/libcoot-coord-utils.la -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/bfkurt.o -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../coot-utils/.libs/libcoot-coord-utils.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcoot-analysis.a bfkurt.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcoot-analysis.a libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/bfactan bfactan.o -Wl,--as-needed ./.libs/libcoot-analysis.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/analysis' Making all in tw make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/tw' /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" 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"libcoot-tw.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o coot-tiddly tiddly.o libcoot-tw.la -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/coot-tiddly tiddly.o -pthread -Wl,--as-needed ./.libs/libcoot-tw.so /usr/lib64/libgtk-x11-2.0.so /usr/lib64/libgdk-x11-2.0.so /usr/lib64/libatk-1.0.so -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 /usr/lib64/libfontconfig.so -lfreetype -lz -lbz2 -lexpat -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -pthread make[1]: Leaving directory 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-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c -o buccaneer-prot.lo buccaneer-prot.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c -o buccaneer-sequence.lo buccaneer-sequence.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c -o cootaneer-sequence.lo cootaneer-sequence.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c buccaneer-prot.cpp -fPIC -DPIC -o .libs/buccaneer-prot.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -fPIC -DPIC -o .libs/cootaneer-sequence.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -fPIC -DPIC -o .libs/buccaneer-sequence.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -fPIC -DPIC -o .libs/buccaneer-lib.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -o buccaneer-lib.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -o cootaneer-sequence.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c buccaneer-prot.cpp -o buccaneer-prot.o >/dev/null 2>&1 mv -f .deps/buccaneer-lib.Tpo .deps/buccaneer-lib.Plo x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT cootaneer-demo.o -MD -MP -MF .deps/cootaneer-demo.Tpo -c -o cootaneer-demo.o cootaneer-demo.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -march=native -O2 -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -o buccaneer-sequence.o >/dev/null 2>&1 mv -f .deps/cootaneer-sequence.Tpo .deps/cootaneer-sequence.Plo mv -f .deps/cootaneer-demo.Tpo .deps/cootaneer-demo.Po mv -f .deps/buccaneer-sequence.Tpo .deps/buccaneer-sequence.Plo mv -f .deps/buccaneer-prot.Tpo .deps/buccaneer-prot.Plo /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcootaneer.la -rpath /usr/lib64 buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtbeginS.o .libs/buccaneer-lib.o .libs/buccaneer-prot.o .libs/buccaneer-sequence.o .libs/cootaneer-sequence.o -Wl,--as-needed -L/usr/lib64 /usr/lib64/libclipper-minimol.so -L/usr/lib /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c -lmmdb /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -Wl,-soname -Wl,libcootaneer.so.0 -o .libs/libcootaneer.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcootaneer.so.0" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so.0") libtool: link: (cd ".libs" && rm -f "libcootaneer.so" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so") libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libcootaneer.a buccaneer-lib.o buccaneer-prot.o buccaneer-sequence.o cootaneer-sequence.o libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libcootaneer.a libtool: link: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o cootaneer-demo cootaneer-demo.o ./libcootaneer.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/cootaneer-demo cootaneer-demo.o -Wl,--as-needed ./.libs/libcootaneer.so -L/usr/lib64 -L/usr/lib /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/cootaneer' Making all in src make[1]: Entering directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/src' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb 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molecule-class-info-refine.o molecule-class-info-refine.cc mv -f .deps/molecule-class-info-other.Tpo .deps/molecule-class-info-other.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 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-DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT molecule-class-info-kk.o -MD -MP -MF .deps/molecule-class-info-kk.Tpo -c -o molecule-class-info-kk.o molecule-class-info-kk.cc mv -f .deps/molecule-class-info-residues.Tpo .deps/molecule-class-info-residues.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include 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-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm 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-I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT molecule-class-info-ncs.o -MD -MP -MF .deps/molecule-class-info-ncs.Tpo -c -o molecule-class-info-ncs.o molecule-class-info-ncs.cc mv -f .deps/molecule-class-info-mutate.Tpo .deps/molecule-class-info-mutate.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 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-I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT xmap-utils.o -MD -MP -MF .deps/xmap-utils.Tpo -c -o xmap-utils.o xmap-utils.cc mv -f .deps/xmap-utils.Tpo .deps/xmap-utils.Po swig -o coot_wrap_python_pre_gtk2.cc -DCOOT_USE_GTK2_INTERFACE -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DUSE_LIBCURL -I../src -shadow -python -c++ ../src/coot.i && mv coot.py coot_gtk2.py mv -f .deps/sequence-view.Tpo .deps/sequence-view.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main 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-I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT density-score-by-residue-src.o -MD -MP -MF .deps/density-score-by-residue-src.Tpo -c -o density-score-by-residue-src.o density-score-by-residue-src.cc mv -f .deps/user-mods.Tpo .deps/user-mods.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT fix-nomenclature.o -MD -MP -MF .deps/fix-nomenclature.Tpo -c -o fix-nomenclature.o fix-nomenclature.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT align.o -MD -MP -MF .deps/align.Tpo -c -o align.o align.cc mv -f .deps/fix-nomenclature.Tpo .deps/fix-nomenclature.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT test-chol.o -MD -MP -MF .deps/test-chol.Tpo -c -o test-chol.o test-chol.cc mv -f .deps/density-score-by-residue-src.Tpo .deps/density-score-by-residue-src.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT test-lbg-graph.o -MD -MP -MF .deps/test-lbg-graph.Tpo -c -o test-lbg-graph.o test-lbg-graph.cc mv -f .deps/test-chol.Tpo .deps/test-chol.Po cp coot_gtk2.py coot.py /bin/sh ../src/post-process-coot-wrap-guile.sh "/usr/bin/guile-config" gtk1 coot_wrap_guile_pre_gtk1.cc coot_wrap_guile_gtk1.cc guile_config: /usr/bin/guile-config guile_version: guile-config - Guile version 1.8.8 gtk2: gtk1 sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/SCM_STRINGP/scm_is_string/ -e s/SCM_STRING_LENGTH/scm_c_string_length/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ -e /.libguile.h./{x;s/.*/#include /;G;} coot_wrap_guile_pre_gtk1.cc ..to.. coot_wrap_guile_pre_gtk1.cc.tmp adding gtk2 and guile ifdefs from coot_wrap_guile_pre_gtk1.cc.tmp coot_wrap_guile_gtk1.cc /bin/sh ../src/post-process-coot-wrap-guile.sh "/usr/bin/guile-config" gtk2 coot_wrap_guile_pre_gtk2.cc coot_wrap_guile_gtk2.cc guile_config: /usr/bin/guile-config guile_version: guile-config - Guile version 1.8.8 gtk2: gtk2 sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/SCM_STRINGP/scm_is_string/ -e s/SCM_STRING_LENGTH/scm_c_string_length/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ -e /.libguile.h./{x;s/.*/#include /;G;} coot_wrap_guile_pre_gtk2.cc ..to.. coot_wrap_guile_pre_gtk2.cc.tmp adding gtk2 and guile ifdefs from coot_wrap_guile_pre_gtk2.cc.tmp coot_wrap_guile_gtk2.cc /bin/sh ../src/post-process-coot-wrap-python.sh gtk2 coot_wrap_python_pre_gtk2.cc coot_wrap_python_gtk2.cc /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o density-score-by-residue-real density-score-by-residue-src.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb -L/usr/lib64 -lgsl -lgslcblas -lm mv -f .deps/test-lbg-graph.Tpo .deps/test-lbg-graph.Po /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/libcoot-ligand.la ../db-main/libcoot-db-main.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib64 -lgsl -lgslcblas -lm -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb mv -f .deps/align.Tpo .deps/align.Po /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-cholesky test-chol.o gl-matrix.o ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb -L/usr/lib64 -lgsl -lgslcblas -lm libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/density-score-by-residue-real density-score-by-residue-src.o -Wl,--as-needed ../geometry/.libs/libcoot-geometry.so -L/usr/lib64 -L/usr/lib ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so -lm -pthread /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-lbg-graph test-lbg-graph.o lbg-graph.o -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o test-lbg-graph test-lbg-graph.o lbg-graph.o -Wl,--as-needed -lmmdb -pthread x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT coot_wrap_guile_gtk1.o -MD -MP -MF .deps/coot_wrap_guile_gtk1.Tpo -c -o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk1.cc libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/test-cholesky test-chol.o gl-matrix.o -Wl,--as-needed ../coords/.libs/libcoot-coords.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lmmdb /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so -lm -pthread libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o -Wl,--as-needed ../ligand/.libs/libcoot-ligand.so -L/usr/lib64 -L/usr/lib /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs/libcoot-ideal.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs/libcoot-db-main.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs/libccp4mg-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-map-utils.so ../db-main/.libs/libcoot-db-main.so ../ideal/.libs/libcoot-ideal.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-coord-extras.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb -pthread mv -f .deps/coot_wrap_guile_gtk1.Tpo .deps/coot_wrap_guile_gtk1.Po x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT coot_wrap_guile_gtk2.o -MD -MP -MF .deps/coot_wrap_guile_gtk2.Tpo -c -o coot_wrap_guile_gtk2.o coot_wrap_guile_gtk2.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../db-main -I../mini-mol -I../ligand -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../lidia-core -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -pthread -DQT_SHARED -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pixman-1 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DCOOT_USE_GTK2_INTERFACE -pthread -DQT_SHARED -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -pthread -DQT_SHARED -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include -pthread -DQT_SHARED -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/qt4 -I/usr/include/qt4/QtGui -I/usr/include/libdrm -I/usr/include/qt4/QtCore -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -MT coot_wrap_python_gtk2.o -MD -MP -MF .deps/coot_wrap_python_gtk2.Tpo -c -o coot_wrap_python_gtk2.o coot_wrap_python_gtk2.cc /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-coot-align align.o coot-align.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/test-coot-align align.o coot-align.o -Wl,--as-needed ../geometry/.libs/libcoot-geometry.so -L/usr/lib64 -L/usr/lib ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lm -lmmdb -pthread mv -f .deps/testing.Tpo .deps/testing.Po mv -f .deps/coot_wrap_guile_gtk2.Tpo .deps/coot_wrap_guile_gtk2.Po mv -f .deps/coot_wrap_python_gtk2.Tpo .deps/coot_wrap_python_gtk2.Po /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o coot-real main.o svn-revision.o c-inner-main.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-pisa.o c-interface-pisa-gui.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-mmdb.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-preferences.o c-interface-refine.o c-interface-scm.o c-interface-superpose.o c-interface-validate.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o geometry-graphs.o get-residue.o flev.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-refmac.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-state.o graphics-info-superpose.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-graph.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o coot_wrap_python_gtk2.o -fopenmp ../ligand/libcoot-ligand.la ../lidia-core/libcoot-lidia-core.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../db-main/libcoot-db-main.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libccp4mg-surface.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../analysis/libcoot-analysis.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la -lguilegtk-2.0 -pthread -L/usr/lib64 -lguile -lltdl -lgmp -lcrypt -lm -lltdl -L/usr/lib64 -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lssm -lmmdb -lmmdb -L/usr/lib64/python2.7/config -lpython2.7 -lutil -Wl,--export-dynamic -pthread -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -lglut -lXmu -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -pthread -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -L/usr/lib64 -lgsl -lgslcblas -lm -lcurl -lssl -lcrypto -lrt -lssl -lcrypto -ldl -lz -lz -lglade-2.0 -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -fopenmp -march=native -O2 -Wl,-O1 -Wl,--hash-style=gnu -o .libs/coot-real main.o svn-revision.o c-inner-main.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-pisa.o c-interface-pisa-gui.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-mmdb.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-preferences.o c-interface-refine.o c-interface-scm.o c-interface-superpose.o c-interface-validate.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o geometry-graphs.o get-residue.o flev.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-refmac.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-state.o graphics-info-superpose.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-graph.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o coot_wrap_python_gtk2.o -fopenmp -pthread -Wl,--export-dynamic -pthread -pthread -pthread -pthread -Wl,--as-needed ../ligand/.libs/libcoot-ligand.so -L/usr/lib64 -L/usr/lib ../lidia-core/.libs/libcoot-lidia-core.so ../density-contour/.libs/libcoot-isosurface.so ../build/.libs/libcoot-cabuild.so ../skeleton/.libs/libcoot-skeleton.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so ../db-main/.libs/libcoot-db-main.so ../high-res/.libs/libcoot-high-res.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ligand/.libs/libcoot-ligand.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ideal/.libs/libcoot-ideal.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/db-main/.libs/libcoot-db-main.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils/.libs/libccp4mg-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs/libcoot-coords.so ../ideal/.libs/libcoot-ideal.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so ../coot-surface/.libs/libcoot-surface.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so ../surface/.libs/libccp4mg-surface.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-heavy.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../analysis/.libs/libcoot-analysis.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../cootaneer/.libs/libcootaneer.so ../compat/.libs/libcoot-compat.so /usr/lib64/libguilegtk-2.0.so /usr/lib64/libguile.so /usr/lib64/libgmp.so -lcrypt /usr/lib64/libltdl.so /usr/lib64/libclipper-minimol.so /usr/lib64/libclipper-mmdb.so /usr/lib64/libclipper-cns.so /usr/lib64/libclipper-cif.so /usr/lib64/libclipper-contrib.so /usr/lib64/libclipper-ccp4.so /usr/lib64/libclipper-phs.so /usr/lib64/libclipper-core.so -lpthread -lccp4c /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so /usr/lib64/libssm.so -lmmdb -L/usr/lib64/python2.7/config -lpython2.7 -lutil /usr/lib64/libgtkglext-x11-1.0.so /usr/lib64/libgdkglext-x11-1.0.so -lGLU -lGL -lXt -lSM -lICE -lpangox-1.0 -lX11 -lglut -lXmu -lgnomecanvas-2 /usr/lib64/libart_lgpl_2.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so -lcurl -lssl -lcrypto -ldl -lglade-2.0 /usr/lib64/libgtk-x11-2.0.so /usr/lib64/libgdk-x11-2.0.so /usr/lib64/libatk-1.0.so -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng14 -lpango-1.0 /usr/lib64/libfontconfig.so -lfreetype -lz -lbz2 -lexpat -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -pthread /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_parallel_start' /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_critical_name_end' /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_loop_dynamic_start' /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_critical_name_start' /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_loop_end_nowait' /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_loop_dynamic_next' /tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs/libccp4mg-surface.so: undefined reference to `GOMP_parallel_end' collect2: ld returned 1 exit status make[1]: *** [coot-real] Error 1 make[1]: Leaving directory `/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/src' make: *** [all-recursive] Error 1 emake failed * ERROR: sci-chemistry/coot-0.6.2 failed (compile phase): * emake failed * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 5838: Called die * The specific snippet of code: * emake || die "emake failed"; * * If you need support, post the output of 'emerge --info =sci-chemistry/coot-0.6.2', * the complete build log and the output of 'emerge -pqv =sci-chemistry/coot-0.6.2'. * The complete build log is located at '/home/ago/log/build/sci-chemistry/coot-0.6.2:20111005-200008.log'. * The ebuild environment file is located at '/tmp/portage/sci-chemistry/coot-0.6.2/temp/environment'. * S: '/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2'