* Package: sci-chemistry/coot-0.8.2-r1  * Repository: gentoo  * Maintainer: sci-chemistry@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp python_targets_python2_7 userland_GNU  * FEATURES: preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... >>> Unpacking coot-0.8.2.tar.gz to /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2 ... * Applying coot-0.8.2-desktop.patch ...  [ ok ] * Applying coot-0.8.2-sandbox-icons.patch ...  [ ok ] * Applying coot-0.8.2-libtool.patch ...  [ ok ] * Applying coot-0.8.2-libguile.patch ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2' ... * Running libtoolize --install --copy --force --automake ...  [ ok ] * Running aclocal -I macros ...  [ ok ] * Running autoconf --force ...  [ ok ] * Running automake --add-missing --copy --force-missing ...  [ ok ] * Running elibtoolize in: coot-0.8.2/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.4.3 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2" * econf: updating coot-0.8.2/config.guess with /usr/share/gnuconfig/config.guess * econf: updating coot-0.8.2/config.sub with /usr/share/gnuconfig/config.sub /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/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 --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/coot-0.8.2-r1 --enable-shared --disable-static --with-goocanvas-prefix=/usr --with-guile=/usr --with-python=/usr --with-guile-gtk --with-pygtk=/usr --with-sqlite3 --with-boost=/usr checking for a BSD-compatible install... /usr/lib/portage/python2.7/ebuild-helpers/xattr/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 whether make supports nested variables... 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 whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none 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... 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(cached) none 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++... none 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/x86_64-pc-linux-gnu-nm -B checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 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/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... mt checking if mt 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... 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(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 which libtool initialization strategy to adopt... AC-PROG-LIBTOOL checking what warning flags to pass to the C compiler... -Wall -Wunused checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused checking what language compliance flags to pass to the C++ compiler... checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking for OpenMP flag of C compiler... -fopenmp checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for GLIB... yes checking if this is MINGW on Windows... no checking for SQLite3... yes checking for mmdb2... yes checking for ssm... yes no checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for Clipper... yes Not using guile checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for GTK... yes checking for GNOME_CANVAS... yes checking for pkg-config... (cached) /usr/bin/x86_64-pc-linux-gnu-pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for glLineWidth in -lGL... yes checking for GLUT... yes checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for PYGTK... yes Good we have pygtk checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib64/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages checking for guile-gtk... checking for boostlib >= 1.20.0... yes checking for python2.7... /usr/bin/python2.7 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib64 -lpython2.7 checking for Python site-packages path... /usr/lib64/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python-2.7-mt... yes checking libglade... yes checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... 7.50.1 Gentoo-Linux-python2.7-gtk2 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating macros/Makefile config.status: creating pdb-templates/Makefile config.status: creating scheme/Makefile config.status: creating python/Makefile config.status: creating compat/Makefile config.status: creating utils/Makefile config.status: creating coot-utils/Makefile config.status: creating protein_db/Makefile config.status: creating ccp4mg-utils/Makefile config.status: creating coords/Makefile config.status: creating db-main/Makefile config.status: creating density-contour/Makefile config.status: creating surface/Makefile config.status: creating coot-surface/Makefile config.status: creating angles/Makefile config.status: creating mini-mol/Makefile config.status: creating skeleton/Makefile config.status: creating ligand/Makefile config.status: creating geometry/Makefile config.status: creating ideal/Makefile config.status: creating build/Makefile config.status: creating analysis/Makefile config.status: creating high-res/Makefile config.status: creating tw/Makefile config.status: creating cootaneer/Makefile config.status: creating cootilus/Makefile config.status: creating greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating lidia-core/Makefile config.status: creating libgtkgraph/Makefile config.status: creating goograph/Makefile config.status: creating lbg/Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/coot config.status: creating python/coot_load_modules.py config.status: creating data/Makefile config.status: creating pixmaps/Makefile config.status: creating pixmaps/icons/Makefile config.status: creating rama-data/Makefile config.status: creating pyrogen/Makefile config.status: creating pyrogen/pyrogen config.status: creating auxil/Makefile config.status: creating auxil/catcheck/Makefile config.status: creating auxil/rama/Makefile config.status: creating auxil/sec-str/Makefile config.status: creating auxil/strand-analysis/Makefile config.status: creating auxil/vectors/Makefile config.status: creating rcrane/Makefile config.status: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2" make -j4 Making all in auxil make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil“ Making all in catcheck make[2]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/catcheck“ make[2]: Pro „all“ nebude nic uděláno. make[2]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/catcheck“ Making all in rama make[2]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/rama“ make[2]: Pro „all“ nebude nic uděláno. make[2]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/rama“ Making all in sec-str make[2]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/sec-str“ make[2]: Pro „all“ nebude nic uděláno. make[2]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/sec-str“ Making all in strand-analysis make[2]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/strand-analysis“ make[2]: Pro „all“ nebude nic uděláno. make[2]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/strand-analysis“ Making all in vectors make[2]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/vectors“ make[2]: Pro „all“ nebude nic uděláno. make[2]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil/vectors“ make[2]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil“ make[2]: Pro „all-am“ nebude nic uděláno. make[2]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil“ make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/auxil“ Making all in scheme make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/scheme“ make[1]: Pro „all“ nebude nic uděláno. make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/scheme“ Making all in python make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/python“ make[1]: Pro „all“ nebude nic uděláno. make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/python“ Making all in pdb-templates make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/pdb-templates“ make[1]: Pro „all“ nebude nic uděláno. make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/pdb-templates“ Making all in macros make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/macros“ make[1]: Pro „all“ nebude nic uděláno. make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/macros“ Making all in compat make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/compat“ /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c -o getopt.lo getopt.c /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c -o getopt1.lo getopt1.c libtool: compile: x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c getopt.c -fPIC -DPIC -o .libs/getopt.o libtool: compile: x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c getopt1.c -fPIC -DPIC -o .libs/getopt1.o /bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -O2 -march=core2 -ggdb -pipe -Wall -Wunused -Wl,-O1 -Wl,--as-needed -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 -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/compat“ Making all in utils make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-utils.lo coot-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-fasta.lo coot-fasta.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o atomic-numbers.lo atomic-numbers.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o gdk-keysyms.lo gdk-keysyms.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-fasta.cc -fPIC -DPIC -o .libs/coot-fasta.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-utils.cc -fPIC -DPIC -o .libs/coot-utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c atomic-numbers.cc -fPIC -DPIC -o .libs/atomic-numbers.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c gdk-keysyms.cc -fPIC -DPIC -o .libs/gdk-keysyms.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o hsv-rgb.lo hsv-rgb.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c hsv-rgb.cc -fPIC -DPIC -o .libs/hsv-rgb.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-utils.la -rpath /usr/lib64 coot-utils.lo coot-fasta.lo atomic-numbers.lo gdk-keysyms.lo hsv-rgb.lo libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/coot-utils.o .libs/coot-fasta.o .libs/atomic-numbers.o .libs/gdk-keysyms.o .libs/hsv-rgb.o -Wl,--as-needed -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils“ Making all in protein_db make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/protein_db“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o protein_db.lo protein_db.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o protein_db_utils.lo protein_db_utils.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o rna_db.lo rna_db.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c protein_db_utils.cpp -fPIC -DPIC -o .libs/protein_db_utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c rna_db.cpp -fPIC -DPIC -o .libs/rna_db.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c protein_db.cpp -fPIC -DPIC -o .libs/protein_db.o protein_db_utils.cpp: In constructor ‘ProteinDB::ScoreClashes::ScoreClashes(const std::vector&, const clipper::Spacegroup&, const clipper::Cell&, double)’: protein_db_utils.cpp:91:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < coords.size(); i++ ) { ^ protein_db_utils.cpp: In member function ‘void ProteinDB::ScoreClashes::set_exclude(const std::vector&, double)’: protein_db_utils.cpp:126:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int a = 0; a < coords.size(); a++ ) { ^ protein_db_utils.cpp:128:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < atoms.size(); i++ ) ^ protein_db_utils.cpp: In member function ‘double ProteinDB::ScoreClashes::score(const ProteinDB::Chain&) const’: protein_db_utils.cpp:176:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < atoms.size(); i++ ) ^ protein_db.cpp: In member function ‘bool ProteinDB::Chain::save_db(clipper::String) const’: protein_db.cpp:244:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < dbresidues.size(); r++ ) { ^ protein_db.cpp: In member function ‘bool ProteinDB::Chain::load_db(clipper::String)’: protein_db.cpp:272:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < dbresidues.size(); r++ ) { ^ protein_db.cpp: In member function ‘bool ProteinDB::Chain::merge(const ProteinDB::Chain&, const std::vector&)’: protein_db.cpp:282:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( wgt.size() != 3*size() ) return false; ^ protein_db.cpp:283:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < dbresidues.size(); r++ ) ^ protein_db.cpp: In member function ‘bool ProteinDB::Chain::is_continuous() const’: protein_db.cpp:303:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbresidues.size()-1; i++ ) { ^ protein_db.cpp: In member function ‘void ProteinDB::Chain::transform(const clipper::RTop_orth&)’: protein_db.cpp:318:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < dbresidues.size(); r++ ) ^ protein_db.cpp: In member function ‘double ProteinDB::Chain::rmsd(const ProteinDB::Chain&) const’: protein_db.cpp:354:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbresidues.size(); i++ ) { ^ protein_db.cpp: In member function ‘double ProteinDB::Chain::rmsd(const ProteinDB::Chain&, const std::vector&) const’: protein_db.cpp:368:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbresidues.size(); i++ ) { ^ protein_db.cpp: In member function ‘void ProteinDB::Chain::debug() const’: protein_db.cpp:382:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < dbresidues.size(); r++ ) { ^ protein_db_utils.cpp: In member function ‘std::vector ProteinDB::ProteinDBSearch::search(const ProteinDB::Chain&, int, ProteinDB::ScoreDensity&, ProteinDB::ScoreClashes&, double, double)’: protein_db_utils.cpp:213:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0; f < frags.size(); f++ ) { ^ protein_db_utils.cpp:228:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0; f < frags.size(); f++ ) { ^ protein_db.cpp: In member function ‘void ProteinDB::ChainDB::calc_distances()’: protein_db.cpp:412:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbresidues.size()-1; i++ ) { ^ protein_db.cpp:425:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbdistvecs.size(); i++ ) { ^ protein_db.cpp: In member function ‘double ProteinDB::ChainDB::score_distance(const ProteinDB::ChainDB&, int, double, const std::vector&) const’: protein_db.cpp:547:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < types.size(); i++ ) ^ protein_db.cpp: In member function ‘std::vector ProteinDB::ChainDB::match_fragment_preliminary(const ProteinDB::ChainDB&, int) const’: protein_db.cpp:566:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbresidues.size(); i++ ) { ^ protein_db.cpp:570:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( scores_dist.size() >= 2*nhit ) { // optimisation ^ protein_db.cpp:582:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( i < scores_dist.size() ) ^ protein_db.cpp: In member function ‘std::vector ProteinDB::ChainDB::match_fragment(const ProteinDB::ChainDB&, int, int) const’: protein_db.cpp:610:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < scores_dist.size(); i++ ) { ^ protein_db.cpp:618:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( scores_lsq.size() > nlsq ) scores_lsq.resize( nlsq ); ^ protein_db.cpp:622:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < scores_lsq.size(); i++ ) { ^ /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-protein-db.la -rpath /usr/lib64 protein_db.lo protein_db_utils.lo rna_db.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/protein_db.o .libs/protein_db_utils.o .libs/rna_db.o -Wl,--as-needed -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -Wl,-soname -Wl,libcoot-protein-db.so.0 -o .libs/libcoot-protein-db.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-protein-db.so.0" && ln -s "libcoot-protein-db.so.0.0.0" "libcoot-protein-db.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-protein-db.so" && ln -s "libcoot-protein-db.so.0.0.0" "libcoot-protein-db.so") libtool: link: ( cd ".libs" && rm -f "libcoot-protein-db.la" && ln -s "../libcoot-protein-db.la" "libcoot-protein-db.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/protein_db“ Making all in mini-mol make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o mini-mol.lo mini-mol.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -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=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o atom-quads.lo atom-quads.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c atom-quads.cc -fPIC -DPIC -o .libs/atom-quads.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c mini-mol-utils.cc -fPIC -DPIC -o .libs/mini-mol-utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c mini-mol.cc -fPIC -DPIC -o .libs/mini-mol.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-mini-mol.la -rpath /usr/lib64 mini-mol.lo mini-mol-utils.lo atom-quads.lo -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o -Wl,--as-needed -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol“ Making all in geometry make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o protein-geometry.lo protein-geometry.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o protein-geometry-mmdb.lo protein-geometry-mmdb.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o read-sbase.lo read-sbase.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o energy-lib.lo energy-lib.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c read-sbase.cc -fPIC -DPIC -o .libs/read-sbase.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c protein-geometry.cc -fPIC -DPIC -o .libs/protein-geometry.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c protein-geometry-mmdb.cc -fPIC -DPIC -o .libs/protein-geometry-mmdb.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c energy-lib.cc -fPIC -DPIC -o .libs/energy-lib.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused 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-DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-tree-extras.lo coot-tree-extras.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 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"-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-tree-extras.cc -fPIC -DPIC -o .libs/coot-tree-extras.o coot-tree-extras.cc: In member function ‘bool coot::atom_tree_t::fill_torsions(const coot::dictionary_residue_restraints_t&, mmdb::Residue*, const string&)’: coot-tree-extras.cc:229:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (iv == quads[iquad].index2) { ^ coot-tree-extras.cc: In member function ‘std::pair > coot::atom_tree_t::get_forward_atoms(const coot::map_index_t&, const coot::map_index_t&) const’: coot-tree-extras.cc:1161:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (index.index() >= atom_vertex_vec.size()) ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" 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.libs/coot-map-heavy.o .libs/coot-fffear.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ./.libs/libcoot-map-utils.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-utils.so ./.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-map-heavy.la" && ln -s "../libcoot-map-heavy.la" "libcoot-map-heavy.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils“ Making all in surface make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/surface“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXSphereElement.lo CXXSphereElement.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXChargeTable.lo CXXChargeTable.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXSphereNode.lo CXXSphereNode.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXCircle.lo CXXCircle.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXChargeTable.cpp -fPIC -DPIC -o .libs/CXXChargeTable.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXSphereNode.cpp -fPIC -DPIC -o .libs/CXXSphereNode.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXCircle.cpp -fPIC -DPIC -o .libs/CXXCircle.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXSphereElement.cpp -fPIC -DPIC -o .libs/CXXSphereElement.o In file included from CXXNewHood.h:22:0, from CXXCircle.cpp:12: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ In file included from CXXNewHood.h:22:0, from CXXSphereElement.cpp:19: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXSphereTriangle.lo CXXSphereTriangle.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXSphereTriangle.cpp -fPIC -DPIC -o .libs/CXXSphereTriangle.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXCircleNode.lo CXXCircleNode.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXSphereTriangleEdge.lo CXXSphereTriangleEdge.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXCircleNode.cpp -fPIC -DPIC -o .libs/CXXCircleNode.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXSphereTriangleEdge.cpp -fPIC -DPIC -o .libs/CXXSphereTriangleEdge.o In file included from CXXNewHood.h:22:0, from CXXCircleNode.cpp:13: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ CXXCircleNode.cpp: In static member function ‘static int CXXCircleNode::probeContacts(std::vector >&, double, std::map > >&)’: CXXCircleNode.cpp:161:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int iCentralProbe = 0; iCentralProbe < centralBin.size(); iCentralProbe++){ ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXCoord.lo CXXCoord.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXCoord.cpp -fPIC -DPIC -o .libs/CXXCoord.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXSurface.lo CXXSurface.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXCreator.lo CXXCreator.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXSurface.cpp -fPIC -DPIC -o .libs/CXXSurface.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXCreator.cpp -fPIC -DPIC -o .libs/CXXCreator.o In file included from CXXNewHood.h:22:0, from CXXSurface.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ CXXSurface.cpp:593:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(nSelAtoms, SelAtom, cout, unitSphereAtOrigin, vdwBallPntrs, contactMap, Conte ^ CXXSurface.cpp:597:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical(cout) ^ CXXSurface.cpp:618:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) ^ CXXSurface.cpp: In member function ‘int CXXSurface::calculateVDWFromAtoms(mmdb::PManager, int, int, double, double, bool)’: CXXSurface.cpp:496:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i(vdwBallPntrs[i]); ^ CXXSurface.cpp:636:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i(contextBallPntrs[i]); ^ CXXSurface.cpp:640:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i(reentrantProbes[i]); ^ CXXSurface.cpp: In member function ‘void CXXSurface::compress(double)’: CXXSurface.cpp:1179:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&, std::vector >&, double, CXXSurface*, int)’: CXXBall.cpp:58:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&, std::vector >&, std::map > >&)’: CXXBall.cpp:201:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int iBall=0; iBall< balls.size(); iBall++){ ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXQADSurfaceStaticData.cpp -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurfaceStaticData.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXSpace.lo CXXSpace.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o CXXUtils.lo CXXUtils.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXSpace.cpp -fPIC -DPIC -o .libs/CXXSpace.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c CXXUtils.cpp -fPIC -DPIC -o .libs/CXXUtils.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -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 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lsrfftw -lsfftw -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/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 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c /usr/lib64/libsrfftw.so -L/usr/lib64 /usr/lib64/libsfftw.so -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -fopenmp -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: ( cd ".libs" && rm -f "libccp4mg-surface.la" && ln -s "../libccp4mg-surface.la" "libccp4mg-surface.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/surface“ Making all in coot-surface make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-surface“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-surface.lo coot-surface.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o rgbreps.lo rgbreps.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-surface.cc -fPIC -DPIC -o .libs/coot-surface.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c rgbreps.cc -fPIC -DPIC -o .libs/rgbreps.o rgbreps.cc: In static member function ‘static int RGBReps::GetColourNumber(std::string)’: rgbreps.cc:71:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i > RGBReps::GetColourDefinitions(std::vector, int)’: rgbreps.cc:112:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int i=0;i< n_codes;i++) { ^ rgbreps.cc:115:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (ii>colours.size()){ ^ /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-surface.la -rpath /usr/lib64 coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL libtool: warning(B: '/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/libsrfftw.la' seems to be moved(B libtool: warning(B: '/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/libsfftw.la' seems to be moved(B libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/surface/.libs -Wl,--as-needed ../surface/.libs/libccp4mg-surface.so -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/usr/lib64 /usr/lib64/libsrfftw.so /usr/lib64/libsfftw.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -fopenmp -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: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-surface“ Making all in lidia-core make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o lbg-shared.lo lbg-shared.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o lbg-molfile.lo lbg-molfile.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o lig-build.lo lig-build.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o rdkit-interface.lo rdkit-interface.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c lig-build.cc -fPIC -DPIC -o .libs/lig-build.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c lbg-molfile.cc -fPIC -DPIC -o .libs/lbg-molfile.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c lbg-shared.cc -fPIC -DPIC -o .libs/lbg-shared.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c rdkit-interface.cc -fPIC -DPIC -o .libs/rdkit-interface.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o cod-types.lo cod-types.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c cod-types.cc -fPIC -DPIC -o .libs/cod-types.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-lidia-core.la -rpath /usr/lib64 lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo cod-types.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la ../coot-utils/libcoot-coord-utils.la libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/lbg-shared.o .libs/lbg-molfile.o .libs/lig-build.o .libs/rdkit-interface.o .libs/cod-types.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -Wl,--as-needed ../geometry/.libs/libcoot-geometry.so ../utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-coord-utils.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-lidia-core.la" && ln -s "../libcoot-lidia-core.la" "libcoot-lidia-core.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core“ Making all in coords make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o Bond_lines.lo Bond_lines.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o Cartesian.lo Cartesian.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 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x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c phenix-geo-bonds.cc -fPIC -DPIC -o .libs/phenix-geo-bonds.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -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 phenix-geo.lo phenix-geo-bonds.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o .libs/phenix-geo.o .libs/phenix-geo-bonds.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../geometry/.libs/libcoot-geometry.so ../coot-utils/.libs/libcoot-shelx.so -L/usr/lib64 ../coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lgsl -lgslcblas ../utils/.libs/libcoot-utils.so -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords“ Making all in angles make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/angles“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -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=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -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=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -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=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c AngleInfo-theta_2-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c AngleInfo.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c AngleInfo-angle-torsions-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -g -O1 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-AngleInfo.la -rpath /usr/lib64 libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/libcoot_AngleInfo_la-AngleInfo.o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o -Wl,--as-needed -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -g -O1 -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/angles“ Making all in skeleton make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/skeleton“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o dm-utils.lo dm-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o graphical_skel.lo graphical_skel.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o BuildCas.lo BuildCas.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c dm-utils.cc -fPIC -DPIC -o .libs/dm-utils.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c graphical_skel.cc -fPIC -DPIC -o .libs/graphical_skel.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c BuildCas.cc -fPIC -DPIC -o .libs/BuildCas.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -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 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/angles/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../angles/.libs/libcoot-AngleInfo.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs/libcoot-lidia-core.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so -lgsl -lgslcblas /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/skeleton“ Making all in ccp4mg-utils make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-utils“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o geomutil.lo geomutil.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o mgtree.lo mgtree.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o cartesian.lo cartesian.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o matrix.lo matrix.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c geomutil.cc -fPIC -DPIC -o .libs/geomutil.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c mgtree.cc -fPIC -DPIC -o .libs/mgtree.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c matrix.cc -fPIC -DPIC -o .libs/matrix.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c cartesian.cc -fPIC -DPIC -o .libs/cartesian.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o quat.lo quat.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o ppmutil.lo ppmutil.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c quat.cc -fPIC -DPIC -o .libs/quat.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c ppmutil.cc -fPIC -DPIC -o .libs/ppmutil.o ppmutil.cc: In member function ‘void image_info::readpng(const char*)’: ppmutil.cc:2508:79: warning: ‘palette’ may be used uninitialized in this function [-Wmaybe-uninitialized] pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; ^ ppmutil.cc:2512:9: warning: ‘num_trans’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(row_pointers[i][j] coot::CalphaBuild::next_ca_by_skel(const std::vector&, const clipper::Coord_grid&, short int, float, const clipper::Xmap&, const clipper::Xmap&, float, const clipper::Xmap&) const’: CalphaBuild.cc:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i coot::CalphaBuild::next_ca_internal(const std::vector&, const clipper::Coord_grid&, short int, float, const clipper::Xmap&, const clipper::Xmap&, float, const clipper::Xmap&, int) const’: CalphaBuild.cc:198:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i coot::CalphaBuild::cluster(const std::vector&, const clipper::Coord_orth&) const’: CalphaBuild.cc:318:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, const std::vector&, const widgeted_molecule_t&, const std::vector&)’: residue-circles.cc:94:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] } while (status == GSL_CONTINUE && iter < n_steps); ^ In file included from lbg.hh:54:0, from wmolecule.cc:33: ../lidia-core/lig-build.hh: In instantiation of ‘std::vector lig_build::molecule_t::bond_indices_with_atom_index(int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’: ../lidia-core/lig-build.hh:1001:79: required from ‘std::vector lig_build::molecule_t::bonds_having_atom_with_atom_index(unsigned int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’ wmolecule.cc:853:38: required from here ../lidia-core/lig-build.hh:746:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (bonds[i].get_atom_1_index() == test_atom_index) { ^ ../lidia-core/lig-build.hh:750:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (bonds[i].get_atom_2_index() == test_atom_index) ^ In file included from lbg.hh:54:0, from lbg.cc:53: ../lidia-core/lig-build.hh: In instantiation of ‘int lig_build::molecule_t::get_bond_index(int, int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’: lbg.cc:1161:51: required from here ../lidia-core/lig-build.hh:765:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] (bonds[i].get_atom_2_index() == atom_index_in_1)) { ^ ../lidia-core/lig-build.hh:764:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((bonds[i].get_atom_1_index() == atom_index_in_1) || ^ ../lidia-core/lig-build.hh:767:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] (bonds[i].get_atom_2_index() == atom_index_in_2)) { ^ ../lidia-core/lig-build.hh:766:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((bonds[i].get_atom_1_index() == atom_index_in_2) || ^ ../lidia-core/lig-build.hh: In instantiation of ‘std::pair > lig_build::molecule_t::find_bonded_atoms_with_no_pass(int, int, int, const std::vector&, int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’: ../lidia-core/lig-build.hh:713:25: required from ‘std::pair > lig_build::molecule_t::found_self_through_bonds(int, int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’ ../lidia-core/lig-build.hh:805:58: required from ‘void lig_build::molecule_t::assign_ring_centres() [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’ wmolecule.cc:135:7: required from here ../lidia-core/lig-build.hh:544:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (bonds[i].get_atom_1_index() == this_atom_index) { ^ ../lidia-core/lig-build.hh:578:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (bonds[i].get_atom_2_index() == this_atom_index) { ^ ../lidia-core/lig-build.hh: In instantiation of ‘std::vector lig_build::molecule_t::bond_indices_with_atom_index(int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’: ../lidia-core/lig-build.hh:1001:79: required from ‘std::vector lig_build::molecule_t::bonds_having_atom_with_atom_index(unsigned int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’ lbg.cc:1320:83: required from here ../lidia-core/lig-build.hh:746:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (bonds[i].get_atom_1_index() == test_atom_index) { ^ ../lidia-core/lig-build.hh:750:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (bonds[i].get_atom_2_index() == test_atom_index) ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o pi-stacking.lo pi-stacking.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c pi-stacking.cc -fPIC -DPIC -o .libs/pi-stacking.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o flev-annotations.lo flev-annotations.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c flev-annotations.cc -fPIC -DPIC -o .libs/flev-annotations.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o lbg-drag-and-drop.lo lbg-drag-and-drop.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c lbg-drag-and-drop.cc -fPIC -DPIC -o .libs/lbg-drag-and-drop.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o qed-interface.lo qed-interface.cc /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o alerts.lo alerts.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c qed-interface.cc -fPIC -DPIC -o .libs/qed-interface.o /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o alerts-list.lo alerts-list.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c alerts.cc -fPIC -DPIC -o .libs/alerts.o x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o lidia-main.o lidia-main.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c alerts-list.cc -fPIC -DPIC -o .libs/alerts-list.o x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-lidia.la -rpath /usr/lib64 lbg.lo wmolecule.lo lbg-search.lo residue-circles.lo pi-stacking.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lmmdb2 -L/usr/lib64 -lgsl -lgslcblas -lm -L/usr/lib -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/lbg.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/pi-stacking.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../coot-utils/.libs/libcoot-coord-utils.so -L/usr/lib64 ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -Wl,-export-dynamic -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-lidia.so.0" && ln -s "libcoot-lidia.so.0.0.0" "libcoot-lidia.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-lidia.so" && ln -s "libcoot-lidia.so.0.0.0" "libcoot-lidia.so") libtool: link: ( cd ".libs" && rm -f "libcoot-lidia.la" && ln -s "../libcoot-lidia.la" "libcoot-lidia.la" ) /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,--export-dynamic -Wl,-O1 -Wl,--as-needed -o lidia lidia-main.o lbg-callbacks-outer.o ./libcoot-lidia.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lmmdb2 -L/usr/lib64 -lgsl -lgslcblas -lm -L/usr/lib -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,--export-dynamic -Wl,-O1 -o .libs/lidia lidia-main.o lbg-callbacks-outer.o -Wl,-export-dynamic -Wl,--as-needed ./.libs/libcoot-lidia.so -L/usr/lib64 -L/usr/lib /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-coord-utils.so ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lm -lutil make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lbg“ Making all in cootaneer make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/cootaneer“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o buccaneer-lib.lo buccaneer-lib.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o buccaneer-prot.lo buccaneer-prot.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o buccaneer-sequence.lo buccaneer-sequence.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o cootaneer-sequence.lo cootaneer-sequence.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c buccaneer-lib.cpp -fPIC -DPIC -o .libs/buccaneer-lib.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c buccaneer-prot.cpp -fPIC -DPIC -o .libs/buccaneer-prot.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c buccaneer-sequence.cpp -fPIC -DPIC -o .libs/buccaneer-sequence.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c cootaneer-sequence.cpp -fPIC -DPIC -o .libs/cootaneer-sequence.o buccaneer-lib.cpp: In member function ‘void LLK_map_target::search(clipper::Xmap&, clipper::Xmap&, clipper::Xmap&, const clipper::Xmap&, const std::vector&) const’: buccaneer-lib.cpp:219:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int op = 0; op < rtops.size(); op++ ) { ^ buccaneer-lib.cpp: In member function ‘clipper::ftype LLK_map_target::Sampled::llk(const clipper::Xmap&, const clipper::RTop_orth&) const’: buccaneer-lib.cpp:274:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < repxyz.size(); i++ ) { ^ buccaneer-lib.cpp: In member function ‘clipper::ftype LLK_map_target::Sampled::correl(const clipper::Xmap&, const clipper::RTop_orth&) const’: buccaneer-lib.cpp:285:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < repxyz.size(); i++ ) { ^ buccaneer-sequence.cpp: In static member function ‘static std::pair > Ca_sequence::sequence_score(const std::vector >&, const clipper::String&)’: buccaneer-sequence.cpp:117:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < scores.size(); r++ ) { ^ buccaneer-sequence.cpp:125:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < score.size(); r++ ) sccum[r+1] = sccum[r]+score[r]; ^ buccaneer-sequence.cpp:131:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r1 = 0; r1 < sccum.size()-minseq; r1++ ) ^ buccaneer-sequence.cpp:132:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r2 = r1+minseq; r2 < sccum.size(); r2++ ) { ^ buccaneer-prot.cpp: In member function ‘clipper::ftype Ca_chain::ramachandran_phi(const int&) const’: buccaneer-prot.cpp:52:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( resno-1 >= 0 && resno < chain.size() ) ^ buccaneer-prot.cpp: In member function ‘clipper::ftype Ca_chain::ramachandran_psi(const int&) const’: buccaneer-prot.cpp:61:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( resno >= 0 && resno+1 < chain.size() ) ^ buccaneer-prot.cpp: In member function ‘std::vector > ProteinLoop::rebuild5atoms(clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth) const’: buccaneer-prot.cpp:169:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int ipsi1 = 0; ipsi1 < ca2s.size(); ipsi1++ ) { ^ buccaneer-prot.cpp:177:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int iphi2 = 0; iphi2 < cc2s.size(); iphi2++ ) { ^ buccaneer-sequence.cpp: In static member function ‘static Score_list Ca_sequence::sequence_match(const std::vector >&, const clipper::MMoleculeSequence&)’: buccaneer-sequence.cpp:199:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < seqmut.size(); j++ ) { ^ buccaneer-prot.cpp: In member function ‘std::vector > ProteinLoop::rebuild8atoms(clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth, clipper::Coord_orth) const’: buccaneer-prot.cpp:214:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < r5.size(); i++ ) { ^ cootaneer-sequence.cpp: In member function ‘std::pair, double> Coot_sequence::sequence_chain(const clipper::Xmap&, const std::vector, std::basic_string > >&, mmdb::Manager&, std::string)’: cootaneer-sequence.cpp:21:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int c = 0; c < sequence.size(); c++ ) { ^ buccaneer-sequence.cpp: In static member function ‘static void Ca_sequence::sequence_apply(clipper::MChain&, const clipper::String&)’: buccaneer-sequence.cpp:307:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( chain.size() != seq.length() ) clipper::Message::message( clipper::Message_fatal( "Sequence: internal error - length ^ buccaneer-prot.cpp: In static member function ‘static std::pair ProteinTools::chain_sequence_match(const clipper::String&, const clipper::MMoleculeSequence&)’: buccaneer-prot.cpp:280:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int res = 0; res < seq[chn].sequence().length(); res++ ) ^ buccaneer-prot.cpp:286:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < chnseq.size(); i++ ) ^ buccaneer-prot.cpp:294:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int chn = 0; chn < seqs.size(); chn++ ) { ^ buccaneer-prot.cpp:298:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < seqs[chn].length(); i++ ) ^ buccaneer-prot.cpp:299:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( i-off >= 0 && i-off < chnseq.length() ) ^ buccaneer-sequence.cpp:342:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < regions.size(); i++ ) { ^ buccaneer-sequence.cpp: In member function ‘bool Ca_sequence::operator()(clipper::MiniMol&, const clipper::MiniMol&, const clipper::Xmap&, const std::vector&, const clipper::MMoleculeSequence&)’: buccaneer-sequence.cpp:380:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int t = 0; t < llktarget.size(); t++ ) ^ buccaneer-prot.cpp: In static member function ‘static bool ProteinTools::chain_tidy(clipper::MiniMol&, const clipper::MiniMol&)’: buccaneer-prot.cpp:364:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( chn < labels1.length() ) { ^ buccaneer-sequence.cpp: In member function ‘clipper::String Ca_sequence::format() const’: buccaneer-sequence.cpp:442:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int chn = 0; chn < history.size(); chn++ ) { ^ buccaneer-sequence.cpp: In member function ‘void Ca_sequence::History::append(const Ca_sequence&)’: buccaneer-sequence.cpp:457:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < data.history.size(); i++ ) ^ buccaneer-sequence.cpp: In member function ‘clipper::String Ca_sequence::History::format(const clipper::MiniMol&) const’: buccaneer-sequence.cpp:465:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int h = 0; h < history.size(); h++ ) { ^ In file included from buccaneer-prot.h:8:0, from buccaneer-sequence.h:5, from buccaneer-sequence.cpp:4: buccaneer-lib.h: In instantiation of ‘void Score_list::add(const ftype&, const T&) [with T = clipper::String; clipper::ftype = double]’: buccaneer-sequence.cpp:106:42: required from here buccaneer-lib.h:32:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( list.size() >= max ) list.pop_back(); ^ buccaneer-lib.h: In instantiation of ‘void Score_list::add(const ftype&, const T&) [with T = std::pair; clipper::ftype = double]’: buccaneer-sequence.cpp:163:72: required from here buccaneer-lib.h:32:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] buccaneer-lib.h: In instantiation of ‘bool Score_list::addable(const ftype&) const [with T = clipper::String; clipper::ftype = double]’: buccaneer-lib.h:31:23: required from ‘void Score_list::add(const ftype&, const T&) [with T = clipper::String; clipper::ftype = double]’ buccaneer-sequence.cpp:106:42: required from here buccaneer-lib.h:28:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] { return ( list.size() < max || score < list.back().first ); } ^ buccaneer-lib.h: In instantiation of ‘bool Score_list::addable(const ftype&) const [with T = std::pair; clipper::ftype = double]’: buccaneer-lib.h:31:23: required from ‘void Score_list::add(const ftype&, const T&) [with T = std::pair; clipper::ftype = double]’ buccaneer-sequence.cpp:163:72: required from here buccaneer-lib.h:28:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcootaneer.la -rpath /usr/lib64 buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/buccaneer-lib.o .libs/buccaneer-prot.o .libs/buccaneer-sequence.o .libs/cootaneer-sequence.o -Wl,--as-needed -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -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: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/cootaneer“ Making all in cootilus make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/cootilus“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o nucleicacid_db.lo nucleicacid_db.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o nautilus-tools.lo nautilus-tools.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o nautilus-ss-find.lo nautilus-ss-find.cpp /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o nautilus-join.lo nautilus-join.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c nucleicacid_db.cpp -fPIC -DPIC -o .libs/nucleicacid_db.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c nautilus-join.cpp -fPIC -DPIC -o .libs/nautilus-join.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c nautilus-ss-find.cpp -fPIC -DPIC -o .libs/nautilus-ss-find.o libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c nautilus-tools.cpp -fPIC -DPIC -o .libs/nautilus-tools.o nautilus-ss-find.cpp: In member function ‘void SSfind::prep_xmap(const clipper::Xmap&, double)’: nautilus-ss-find.cpp:19:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < mapbox.size(); i++ ) { ^ nautilus-ss-find.cpp: In member function ‘std::vector SSfind::search(const std::vector >&, const std::vector&, double, double) const’: nautilus-ss-find.cpp:59:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < ops.size(); r++ ) { ^ nautilus-ss-find.cpp:62:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < target_cs.size(); i++ ) { ^ nautilus-ss-find.cpp:74:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < rslts.size(); i++ ) rslts[i].trn = srctrn[i]; ^ nautilus-ss-find.cpp:79:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < rslts.size(); i++ ) { // loop over map ^ nautilus-ss-find.cpp:86:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < index_lists.size(); r++ ) { // loop over rotns ^ nautilus-ss-find.cpp:95:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( !( i < index_list.size() ) ) break; ^ nautilus-ss-find.cpp:110:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < rslts.size(); i++ ) ^ nucleicacid_db.cpp: In member function ‘bool NucleicAcidDB::Chain::is_continuous() const’: nucleicacid_db.cpp:448:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < dbmonomers.size()-1; i++ ) { ^ nucleicacid_db.cpp: In member function ‘void NucleicAcidDB::Chain::transform(const clipper::RTop_orth&)’: nucleicacid_db.cpp:462:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < dbmonomers.size(); r++ ) ^ nautilus-tools.cpp: In static member function ‘static clipper::MiniMol NucleicAcidTools::flag_chains(const clipper::MiniMol&)’: nautilus-tools.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 1; r < flag.size()-1; r++ ) ^ nautilus-tools.cpp: In static member function ‘static clipper::RTop_orth NucleicAcidTools::symmetry_rtop(const std::vector&, clipper::Coord_orth&, const clipper::Spacegroup&, const clipper::Cell&)’: nautilus-tools.cpp:81:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int a = 0; a < cowrk.size(); a++ ) ^ nautilus-tools.cpp:89:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int a = 0; a < cwrk.size(); a++ ) { ^ nautilus-tools.cpp: In static member function ‘static bool NucleicAcidTools::symm_match(clipper::MiniMol&, const clipper::MiniMol&)’: nautilus-tools.cpp:139:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < atomr.size(); i++ ) { ^ nautilus-tools.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int a = 0; a < atomw.size(); a++ ) { ^ nautilus-tools.cpp:192:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int a = 0; a < atomw.size(); a++ ) { ^ nautilus-join.cpp: In static member function ‘static std::vector NucleicAcidJoin::best_chain(std::vector&)’: nautilus-join.cpp:21:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < node_score.size(); i++ ) ^ nautilus-join.cpp:31:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < nodes[node].ptrs.size(); j++ ) { ^ nautilus-join.cpp:57:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 1; i < node_score.size(); i++ ) ^ nautilus-join.cpp: In static member function ‘static clipper::MiniMol NucleicAcidJoin::join(const clipper::MiniMol&)’: nautilus-join.cpp:103:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < nas.size(); r++ ) { ^ nautilus-join.cpp:114:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < nas.size(); r++ ) equivalent[r] = r; ^ nautilus-join.cpp:128:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < atoms.size(); i++ ) { // find other equivalent NAs ^ nautilus-join.cpp:155:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r1 = 0; r1 < nas.size()-1; r1++ ) { ^ nautilus-join.cpp:167:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < joins[e1].ptrs.size(); i++ ) ^ nautilus-join.cpp:194:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < chn.size(); r++ ) ^ nautilus-join.cpp:197:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0; f < joins.size(); f++ ) ^ nautilus-join.cpp:201:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0; f < joins.size(); f++ ) ^ nautilus-join.cpp:216:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int c = 0; c < chns.size(); c++ ) { ^ nautilus-join.cpp:220:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int r = 0; r < chns[c].size(); r++ ) { ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o nautilus-target.lo nautilus-target.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c nautilus-target.cpp -fPIC -DPIC -o .libs/nautilus-target.o nautilus-target.cpp: In member function ‘double NucleicAcidTarget::radius() const’: nautilus-target.cpp:48:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < target_.size(); i++ ) { ^ nautilus-target.cpp:53:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int a = 0; a < coords.size(); a++ ) { ^ nautilus-target.cpp: In member function ‘float NucleicAcidTarget::score_min(const clipper::Xmap&, const clipper::RTop_orth&) const’: nautilus-target.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < target_.size(); i++ ) { ^ nautilus-target.cpp: In member function ‘float NucleicAcidTarget::score_sum(const clipper::Xmap&, const clipper::RTop_orth&) const’: nautilus-target.cpp:77:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < target_.size(); i++ ) { ^ nautilus-target.cpp: In member function ‘const clipper::MiniMol NucleicAcidTargets::find(const clipper::Xmap&, const clipper::MiniMol&, int, int, double)’: nautilus-target.cpp:452:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < found_s.size(); i++ ) { ^ nautilus-target.cpp:458:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < found_p.size(); i++ ) { ^ nautilus-target.cpp: In member function ‘const clipper::MiniMol NucleicAcidTargets::prune(const clipper::MiniMol&) const’: nautilus-target.cpp:577:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < atoms.size(); i++ ) { ^ nautilus-target.cpp: In member function ‘const clipper::MiniMol NucleicAcidTargets::rebuild_bases(const clipper::Xmap&, const clipper::MiniMol&) const’: nautilus-target.cpp:718:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0; i < atoms.size(); i++ ) { ^ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o cootilus-build.lo cootilus-build.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c cootilus-build.cpp -fPIC -DPIC -o .libs/cootilus-build.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcootilus.la -rpath /usr/lib64 nucleicacid_db.lo nautilus-tools.lo nautilus-ss-find.lo nautilus-join.lo nautilus-target.lo cootilus-build.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/nucleicacid_db.o .libs/nautilus-tools.o .libs/nautilus-ss-find.o .libs/nautilus-join.o .libs/nautilus-target.o .libs/cootilus-build.o -Wl,--as-needed -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -Wl,-soname -Wl,libcootilus.so.0 -o .libs/libcootilus.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcootilus.so.0" && ln -s "libcootilus.so.0.0.0" "libcootilus.so.0") libtool: link: (cd ".libs" && rm -f "libcootilus.so" && ln -s "libcootilus.so.0.0.0" "libcootilus.so") libtool: link: ( cd ".libs" && rm -f "libcootilus.la" && ln -s "../libcootilus.la" "libcootilus.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/cootilus“ Making all in goograph make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/goograph“ /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o goograph.lo goograph.cc libtool: compile: x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" "-DPACKAGE_STRING=\"coot 0.8.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c goograph.cc -fPIC -DPIC -o .libs/goograph.o /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -Wl,--as-needed -o libcoot-goograph.la -rpath /usr/lib64 goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -L/usr/lib -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o .libs/goograph.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lidia-core/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../lidia-core/.libs/libcoot-lidia-core.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas ../utils/.libs/libcoot-utils.so -L/usr/lib -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crtn.o -O2 -march=core2 -ggdb -Wl,-O1 -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-goograph.so.0" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-goograph.so" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so") libtool: link: ( cd ".libs" && rm -f "libcoot-goograph.la" && ln -s "../libcoot-goograph.la" "libcoot-goograph.la" ) make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/goograph“ Making all in pyrogen make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/pyrogen“ make[1]: Pro „all“ nebude nic uděláno. make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/pyrogen“ Making all in src make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/src“ x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o density-score-by-residue-src.o density-score-by-residue-src.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o fix-nomenclature.o fix-nomenclature.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-nomenclature.o coot-nomenclature.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o main.o main.cc main.cc: In function ‘int main(int, char**)’: main.cc:200:7: warning: ‘void g_type_init()’ is deprecated (declared at /usr/include/glib-2.0/gobject/gtype.h:681) [-Wdeprecated-declarations] g_type_init(); // for lbg command-line mode, so that ^ main.cc:200:19: warning: ‘void g_type_init()’ is deprecated (declared at /usr/include/glib-2.0/gobject/gtype.h:681) [-Wdeprecated-declarations] g_type_init(); // for lbg command-line mode, so that ^ x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o atom-overlaps.o atom-overlaps.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" 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-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-build-gui.o c-interface-build-gui.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo 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-DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-database.o c-interface-database.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 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-DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-gui.o c-interface-gui.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 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-DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-gtk2.o c-interface-gtk2.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK 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-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-info.o c-interface-info.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-kk.o c-interface-kk.cc In file included from /usr/include/python2.7/Python.h:80:0, from c-interface-info.cc:29: c-interface-info.cc: In function ‘PyObject* map_parameters_py(int)’: /usr/include/python2.7/object.h:769:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ^ c-interface-info.cc:3171:9: note: in expansion of macro ‘Py_INCREF’ Py_INCREF(Py_True); ^ /usr/include/python2.7/object.h:769:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ^ c-interface-info.cc:3174:9: note: in expansion of macro ‘Py_INCREF’ Py_INCREF(Py_False); ^ x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-ligands.o c-interface-ligands.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-ligands-gui.o c-interface-ligands-gui.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-maps.o c-interface-maps.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 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-DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-pisa.o c-interface-pisa.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 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-DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-pisa-gui.o c-interface-pisa-gui.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o c-interface-preferences.o c-interface-preferences.cc c-interface-preferences.cc: In function ‘int preferences_internal_font_own_colour_flag()’: c-interface-preferences.cc:1552:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iob_refcnt++) ^ /usr/include/python2.7/object.h:824:54: note: in expansion of macro ‘Py_INCREF’ #define Py_XINCREF(op) do { if ((op) == NULL) ; else Py_INCREF(op); } while (0) ^ c-interface.cc:5698:4: note: in expansion of macro ‘Py_XINCREF’ Py_XINCREF(Py_True); ^ x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz 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-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c -o callbacks.o callbacks.c x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o change-dir.o change-dir.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 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-I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o cmtz-interface.o cmtz-interface.cc 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-DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-align.o coot-align.cc x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c -o coot-glue.o coot-glue.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -march=core2 -ggdb -pipe -Wall -Wunused -c -o coot-glue-gtk2.o coot-glue-gtk2.c x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.2\" -DPACKAGE_STRING=\"coot\ 0.8.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DHAVE_GNOME_CANVAS -pthread -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DCOOT_USE_GTK2_INTERFACE -pthread -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/libdrm -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libglade-2.0 -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DHAVE_SSMLIB -I/usr/include -pthread -I/usr/include/pygtk-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -DUSE_SQLITE3 -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib64/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Gentoo-Linux-python2.7-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE_GTK -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c -o coot-hydrogens.o coot-hydrogens.cc coot-glue-gtk2.c:8:22: fatal error: libguile.h: Adresář nebo soubor neexistuje #include ^ compilation terminated. make[1]: *** [Makefile:1446: coot-glue-gtk2.o] Chyba 1 make[1]: *** Čeká se na nedokončené úlohy… make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/src“ make: *** [Makefile:697: all-recursive] Chyba 1 * ERROR: sci-chemistry/coot-0.8.2-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/coot-0.8.2-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/coot-0.8.2-r1::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2' * S: '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2'