build.log

build.log (text/plain), 602.38 KB, created by David Kredba on 2016-08-16 18:05:19 UTC

[32;01m * [39;49;00mPackage:    sci-chemistry/coot-0.8.2-r1
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux openmp python_targets_python2_7 userland_GNU
[32;01m * [39;49;00mFEATURES:   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 ...
 [32;01m*[0m Applying coot-0.8.2-desktop.patch ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.8.2-sandbox-icons.patch ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.8.2-libtool.patch ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying coot-0.8.2-libguile.patch ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2' ...
 [32;01m*[0m Running libtoolize --install --copy --force --automake ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running aclocal -I macros ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf --force ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy --force-missing ...
[A[116C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running elibtoolize in: coot-0.8.2/
 [32;01m*[0m   Applying portage/1.2.0 patch ...
 [32;01m*[0m   Applying sed/1.5.6 patch ...
 [32;01m*[0m   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... (cached) none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes
checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes
checking dependency style of x86_64-pc-linux-gnu-gcc... (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... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking 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<clipper::Coord_orth>&, 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<clipper::Coord_orth>&, 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<double>&)’:
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<double>&) 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::Chain> 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<ProteinDB::Residue::TypeMask>&) 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<int> 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::Chain> 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
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make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry“
Making all in coot-utils
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils“
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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 -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-shelx-ins.cc  -fPIC -DPIC -o .libs/coot-shelx-ins.o
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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 -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-coord-extras.cc  -fPIC -DPIC -o .libs/coot-coord-extras.o
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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 -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-coord-lsq.cc  -fPIC -DPIC -o .libs/coot-coord-lsq.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.. -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<int, std::vector<coot::map_index_t> > 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())
                      ^
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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-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o .libs/coot-h-bonds.o .libs/hole.o .libs/read-sm-cif.o .libs/bonded-pairs.o .libs/helix-analysis.o .libs/elastic.o .libs/glyco-torsions.o .libs/coot-least-squares.o .libs/atom-overlaps.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/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/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 /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 -L/usr/lib64 -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-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-coord-utils.so.0" && ln -s "libcoot-coord-utils.so.0.0.0" "libcoot-coord-utils.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-coord-utils.so" && ln -s "libcoot-coord-utils.so.0.0.0" "libcoot-coord-utils.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-coord-utils.la" && ln -s "../libcoot-coord-utils.la" "libcoot-coord-utils.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o libcoot-shelx.la -rpath /usr/lib64 coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-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/coot-shelx-ins.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/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-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 ../utils/.libs/libcoot-utils.so -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-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-shelx.so.0" && ln -s "libcoot-shelx.so.0.0.0" "libcoot-shelx.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-shelx.so" && ln -s "libcoot-shelx.so.0.0.0" "libcoot-shelx.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-shelx.la" && ln -s "../libcoot-shelx.la" "libcoot-shelx.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o libcoot-coord-extras.la -rpath /usr/lib64 coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo libcoot-coord-utils.la  
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-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o .libs/water-coordination.o .libs/lsq-improve.o .libs/coot-coord-utils-glyco.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/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-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-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-coord-extras.so.0" && ln -s "libcoot-coord-extras.so.0.0.0" "libcoot-coord-extras.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-coord-extras.so" && ln -s "libcoot-coord-extras.so.0.0.0" "libcoot-coord-extras.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-coord-extras.la" && ln -s "../libcoot-coord-extras.la" "libcoot-coord-extras.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o libcoot-map-utils.la -rpath /usr/lib64 coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo 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/coot-map-utils.o .libs/peak-search.o .libs/peak-search-from-list.o .libs/trim.o .libs/xmap-stats.o .libs/maps-spherical.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/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-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-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-map-utils.so.0" && ln -s "libcoot-map-utils.so.0.0.0" "libcoot-map-utils.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-map-utils.so" && ln -s "libcoot-map-utils.so.0.0.0" "libcoot-map-utils.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-map-utils.la" && ln -s "../libcoot-map-utils.la" "libcoot-map-utils.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o libcoot-map-heavy.la -rpath /usr/lib64 coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la -L/usr/lib64 -lgsl -lgslcblas -lm 
libtool: link: x86_64-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o  .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<CXXCircleNode, CXX::CXXAlloc<CXXCircleNode> >&, double, std::map<CXXCircleNode*, std::vector<CXXCircleNode*, CXX::CXXAlloc<CXXCircleNode*> > >&)’:
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.size(); i++){
                 ^
CXXSurface.cpp:497:45: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete vdwBallPntrs[i];
                                             ^
CXXSurface.cpp:499:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<contextBallPntrs.size(); i++){
                 ^
CXXSurface.cpp:502:54: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
    if (contextBallPntrs[i]) delete contextBallPntrs[i];
                                                      ^
CXXSurface.cpp: In member function ‘int CXXSurface::calculateAccessibleFromAtoms(mmdb::PManager, int, int, double, double, bool)’:
CXXSurface.cpp:548:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<vdwBallPntrs.size(); i++){
                 ^
CXXSurface.cpp:549:45: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete vdwBallPntrs[i];
                                             ^
CXXSurface.cpp:551:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<contextBallPntrs.size(); i++){
                 ^
CXXSurface.cpp:554:54: warning: deleting object of abstract class type ‘CXXBall’ which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
    if (contextBallPntrs[i]) delete contextBallPntrs[i];
                                                      ^
CXXSurface.cpp: In member function ‘int CXXSurface::calculateFromAtoms(mmdb::PManager, int, int, double, double, bool)’:
CXXSurface.cpp:633:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<vdwBallPntrs.size(); i++){
                    ^
CXXSurface.cpp:634:79: warning: deleting object of polymorphic class type ‘CXXAtomBall’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (vdwBallPntrs[i]) delete static_cast<const CXXAtomBall *>(vdwBallPntrs[i]);
                                                                               ^
CXXSurface.cpp:636:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<contextBallPntrs.size(); i++){
                 ^
CXXSurface.cpp:637:87: warning: deleting object of polymorphic class type ‘CXXAtomBall’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
   if (contextBallPntrs[i]) delete static_cast<const CXXAtomBall *>(contextBallPntrs[i]);
                                                                                       ^
CXXSurface.cpp:640:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<reentrantProbes.size(); i++){
                 ^
CXXSurface.cpp:641:71: warning: deleting object of polymorphic class type ‘CXXReentrantProbeBall’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
   delete static_cast<const CXXReentrantProbeBall *>(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<vertices.size(); i++){
                 ^
CXXSurface.cpp:1181:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j<compressedVertices.size() && uniqueAndDrawn; j++){
                  ^
CXXSurface.cpp:1197:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<triangles.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.  -I../coot-utils       -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o CXXSurfaceVertex.lo CXXSurfaceVertex.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 CXXSurfaceVertex.cpp  -fPIC -DPIC -o .libs/CXXSurfaceVertex.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 CXXException.lo CXXException.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 CXXException.cpp  -fPIC -DPIC -o .libs/CXXException.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 CXXTorusElement.lo CXXTorusElement.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 CXXFFTSolventMap.lo CXXFFTSolventMap.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 CXXTorusNode.lo CXXTorusNode.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 CXXFFTSolventMap.cpp  -fPIC -DPIC -o .libs/CXXFFTSolventMap.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 CXXTorusElement.cpp  -fPIC -DPIC -o .libs/CXXTorusElement.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 CXXTorusNode.cpp  -fPIC -DPIC -o .libs/CXXTorusNode.o
In file included from CXXNewHood.h:22:0,
                 from CXXTorusElement.cpp:17:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin) 
 ^
/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 CXXFortranFile.lo CXXFortranFile.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 CXXFortranFile.cpp  -fPIC -DPIC -o .libs/CXXFortranFile.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 CXXNewHood.lo CXXNewHood.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 CXXNewHood.cpp  -fPIC -DPIC -o .libs/CXXNewHood.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 CXXTriangle.lo CXXTriangle.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 CXXNode.lo CXXNode.cpp
In file included from CXXNewHood.h:22:0,
                 from CXXNewHood.cpp:15:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin) 
 ^
CXXNewHood.cpp:345:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (circleNodes)
 ^
CXXNewHood.cpp:376:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (mainTriangles)
 ^
CXXNewHood.cpp:409:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (mainTriangles)
 ^
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 CXXTriangle.cpp  -fPIC -DPIC -o .libs/CXXTriangle.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 CXXNode.cpp  -fPIC -DPIC -o .libs/CXXNode.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 CXXQADSurface.lo CXXQADSurface.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 CXXBall.lo CXXBall.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 CXXQADSurface.cpp  -fPIC -DPIC -o .libs/CXXQADSurface.o
In file included from CXXNewHood.h:22:0,
                 from CXXQADSurface.h:11,
                 from CXXQADSurface.cpp:1:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin) 
 ^
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 CXXBall.cpp  -fPIC -DPIC -o .libs/CXXBall.o
In file included from CXXBall.cpp:10:0:
CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical (unitSphereAtOrigin) 
 ^
CXXBall.cpp:34:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared(delta, nBalls, contactMap, aSurface, raggedEdges, insideOrOutside, ballPntrs)
 ^
CXXBall.cpp:83:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared(trimmedBalls, contactMap, insideOrOutside, reformattedEdges, delta, aSurface)
 ^
CXXBall.cpp:197:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(none) shared (binnedballs, ballRadiusX2, limits, binWidth, nBins, balls, contactMap) sched
 ^
CXXBall.cpp: In static member function ‘static int CXXBall::triangulateBalls(std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, double, CXXSurface*, int)’:
CXXBall.cpp:58:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<raggedEdges.size(); i++){
                 ^
CXXBall.cpp:84:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<trimmedBalls.size(); i++){
                 ^
CXXBall.cpp: In static member function ‘static int CXXBall::ballContacts(std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> >&, std::map<const CXXBall*, std::vector<const CXXBall*, CXX::CXXAlloc<const CXXBall*> > >&)’:
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<colours_name_map.size();i++) {
                 ^
rgbreps.cc: In static member function ‘static std::vector<std::vector<double> > RGBReps::GetColourDefinitions(std::vector<int>, 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: [31mwarning(B[m: [1m'/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/libsrfftw.la' seems to be moved(B[m
libtool: [31mwarning(B[m: [1m'/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/libsfftw.la' seems to be moved(B[m
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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“
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/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
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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\" -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 cos-sin.lo cos-sin.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 mmdb-extras.lo mmdb-extras.cc
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/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]<num_trans){
         ^
ppmutil.cc:2513:86: warning: ‘trans_alpha’ may be used uninitialized in this function [-Wmaybe-uninitialized]
          pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
                                                                                      ^
/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-utils.la -rpath /usr/lib64 geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo -lpng 
libtool: link: x86_64-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o  .libs/geomutil.o .libs/mgtree.o .libs/cartesian.o .libs/matrix.o .libs/quat.o .libs/ppmutil.o   -Wl,--as-needed -lpng -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4 -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,libccp4mg-utils.so.0 -o .libs/libccp4mg-utils.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so.0" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so.0")
libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so")
libtool: link: ( cd ".libs" && rm -f "libccp4mg-utils.la" && ln -s "../libccp4mg-utils.la" "libccp4mg-utils.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-utils“
Making all in density-contour
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/density-contour“
/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 Vectors.lo Vectors.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..     -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o CIsoSurface.lo CIsoSurface.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..     -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o density-contour-triangles.lo density-contour-triangles.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 Vectors.cpp  -fPIC -DPIC -o .libs/Vectors.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 CIsoSurface.cpp  -fPIC -DPIC -o .libs/CIsoSurface.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 density-contour-triangles.cc  -fPIC -DPIC -o .libs/density-contour-triangles.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-isosurface.la -rpath /usr/lib64 Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -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/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o   -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/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/lidia-core/.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 ../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-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so.0" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-isosurface.la" && ln -s "../libcoot-isosurface.la" "libcoot-isosurface.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/density-contour“
Making all in db-main
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/db-main“
/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 db-main.lo db-main.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 db-strands.lo db-strands.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\" -DDATADIR=\"/usr/share\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c db-strands.cc  -fPIC -DPIC -o .libs/db-strands.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\" -DDATADIR=\"/usr/share\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c db-main.cc  -fPIC -DPIC -o .libs/db-main.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-db-main.la -rpath /usr/lib64 db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la -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/db-main.o .libs/db-strands.o   -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/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/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/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../mini-mol/.libs/libcoot-mini-mol.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 -lgsl -lgslcblas ../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-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so.0" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-db-main.la" && ln -s "../libcoot-db-main.la" "libcoot-db-main.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/db-main“
Making all in ideal
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ideal“
/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_GSL -I/usr/include    -DHAVE_GSL  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o simple-restraint.lo simple-restraint.cc
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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_GSL -I/usr/include -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c parallel-planes.cc  -fPIC -DPIC -o .libs/parallel-planes.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..    -DHAVE_GSL -I/usr/include    -DHAVE_GSL  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o mini-rsr.o mini-rsr.cc
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include    -DHAVE_GSL  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o libcoot-ideal.la -rpath /usr/lib64 simple-restraint.lo chirals.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo coot-compare-residues.lo link-restraints.lo parallel-planes.lo ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/lib64 -lgsl -lgslcblas -lm 
libtool: link: x86_64-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o  .libs/simple-restraint.o .libs/chirals.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o .libs/torsion-bonds.o .libs/coot-compare-residues.o .libs/link-restraints.o .libs/parallel-planes.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/coords/.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 -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/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/lidia-core/.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 ../coot-utils/.libs/libcoot-map-heavy.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /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 ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-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 -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-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-ideal.so.0" && ln -s "libcoot-ideal.so.0.0.0" "libcoot-ideal.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-ideal.so" && ln -s "libcoot-ideal.so.0.0.0" "libcoot-ideal.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-ideal.la" && ln -s "../libcoot-ideal.la" "libcoot-ideal.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include    -DHAVE_GSL  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2  -Wl,-O1 -Wl,--as-needed -o mini-rsr mini-rsr.o ./libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la ../mini-mol/libcoot-mini-mol.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 
libtool: link: x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -o .libs/mini-rsr mini-rsr.o  -Wl,--as-needed ./.libs/libcoot-ideal.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /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 ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-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 ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so ../mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lm
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ideal“
Making all in ligand
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ligand“
/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_GSL -I/usr/include      -DPKGDATADIR='"/usr/share/coot"'  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o ligand.lo ligand.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.. -DHAVE_GSL -I/usr/include      -DPKGDATADIR='"/usr/share/coot"'  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o ligand-extras.lo ligand-extras.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.. -DHAVE_GSL -I/usr/include      -DPKGDATADIR='"/usr/share/coot"'  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o residue_by_phi_psi.lo residue_by_phi_psi.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.. -DHAVE_GSL -I/usr/include      -DPKGDATADIR='"/usr/share/coot"'  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o wiggly-ligand.lo wiggly-ligand.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_GSL -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c residue_by_phi_psi.cc  -fPIC -DPIC -o .libs/residue_by_phi_psi.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.. -DHAVE_GSL -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c wiggly-ligand.cc  -fPIC -DPIC -o .libs/wiggly-ligand.o
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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/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o   -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ideal/.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/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/db-main/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-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/coords/.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/lidia-core/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../ideal/.libs/libcoot-ideal.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-utils.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../coords/.libs/libcoot-coords.so /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 ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.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 -lgsl -lgslcblas ../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-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++  -DPKGDATADIR='"/usr/share/coot"'  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o findligand-real find-ligand.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.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 
/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 findwaters-real find-waters.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.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 
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libtool: link: x86_64-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -o .libs/findligand-real find-ligand.o  -Wl,--as-needed ./.libs/libcoot-ligand.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-utils/.libs/libccp4mg-utils.so ../ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /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 ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-shelx.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 ../mini-mol/.libs/libcoot-mini-mol.so ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lgsl -lgslcblas -lm
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ligand“
Making all in high-res
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/high-res“
/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_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o high-res.lo high-res.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..    -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o coot-atom-graph.lo coot-atom-graph.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..    -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o residue-distortions.lo residue-distortions.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..    -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o sequence-assignment.lo sequence-assignment.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_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c residue-distortions.cc  -fPIC -DPIC -o .libs/residue-distortions.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.. -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c sequence-assignment.cc  -fPIC -DPIC -o .libs/sequence-assignment.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.. -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c high-res.cc  -fPIC -DPIC -o .libs/high-res.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.. -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c coot-atom-graph.cc  -fPIC -DPIC -o .libs/coot-atom-graph.o
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o libcoot-high-res.la -rpath /usr/lib64 high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -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/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o   -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/ligand/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ideal/.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/db-main/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-utils/.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/lidia-core/.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/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/ideal/.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/db-main/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords/.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/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/utils/.libs -Wl,--as-needed ../mini-mol/.libs/libcoot-mini-mol.so ../ligand/.libs/libcoot-ligand.so -L/usr/lib64 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-heavy.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/ccp4mg-utils/.libs/libccp4mg-utils.so -lpng /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coords/.libs/libcoot-coords.so /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-extras.so /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/coot-utils/.libs/libcoot-map-utils.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-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so.0" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/high-res“
Making all in build
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/build“
/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 CalphaBuild.lo CalphaBuild.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 CalphaBuild.cc  -fPIC -DPIC -o .libs/CalphaBuild.o
CalphaBuild.cc: In member function ‘std::vector<coot::scored_skel_coord> coot::CalphaBuild::next_ca_by_skel(const std::vector<clipper::Coord_orth>&, const clipper::Coord_grid&, short int, float, const clipper::Xmap<int>&, const clipper::Xmap<float>&, float, const clipper::Xmap<coot::SkeletonTreeNode>&) const’:
CalphaBuild.cc:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<scored_positions.size(); i++) { 
                   ^
CalphaBuild.cc: In member function ‘std::vector<coot::scored_skel_coord> coot::CalphaBuild::next_ca_internal(const std::vector<clipper::Coord_orth>&, const clipper::Coord_grid&, short int, float, const clipper::Xmap<int>&, const clipper::Xmap<float>&, float, const clipper::Xmap<coot::SkeletonTreeNode>&, int) const’:
CalphaBuild.cc:198:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i=0; i<ssc.size(); i++) {
                     ^
CalphaBuild.cc:237:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i=0; i<ssc.size(); i++) {
                     ^
CalphaBuild.cc: In member function ‘std::vector<coot::scored_skel_coord> coot::CalphaBuild::cluster(const std::vector<coot::scored_skel_coord>&, const clipper::Coord_orth&) const’:
CalphaBuild.cc:318:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i=0; i<interesting.size(); i++) {
                   ^
CalphaBuild.cc:322:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0; j<sum_centres.size(); j++) {
                      ^
CalphaBuild.cc:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int j=0; j<sum_centres.size(); j++) {
                   ^
/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-cabuild.la -rpath /usr/lib64 CalphaBuild.lo ../angles/libcoot-AngleInfo.la -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/CalphaBuild.o   -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/angles/.libs -Wl,--as-needed ../angles/.libs/libcoot-AngleInfo.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-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so.0" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-cabuild.la" && ln -s "../libcoot-cabuild.la" "libcoot-cabuild.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/build“
Making all in greg-tests
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/greg-tests“
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/greg-tests“
Making all in python-tests
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/python-tests“
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-tests“
Making all in analysis
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/analysis“
/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 bfkurt.lo bfkurt.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 mogul.lo mogul.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 kolmogorov.lo kolmogorov.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 stats.lo stats.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 bfkurt.cc  -fPIC -DPIC -o .libs/bfkurt.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 mogul.cc  -fPIC -DPIC -o .libs/mogul.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 kolmogorov.cc  -fPIC -DPIC -o .libs/kolmogorov.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 stats.cc  -fPIC -DPIC -o .libs/stats.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 cablam.lo cablam.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..     -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o bfactan.o bfactan.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 cablam.cc  -fPIC -DPIC -o .libs/cablam.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-analysis.la -rpath /usr/lib64 bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2 -L/usr/lib64 -lgsl -lgslcblas -lm 
libtool: link: x86_64-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/crtbeginS.o  .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.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/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 /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/geometry/.libs/libcoot-geometry.so ../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 ../mini-mol/.libs/libcoot-mini-mol.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c ../utils/.libs/libcoot-utils.so -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-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++  -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused   -Wl,-O1 -Wl,--as-needed -o bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.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 
libtool: link: x86_64-pc-linux-gnu-g++ -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -Wl,-O1 -o .libs/bfactan bfactan.o  -Wl,--as-needed ./.libs/libcoot-analysis.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 ../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 -lgsl -lgslcblas ../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 ../mini-mol/.libs/libcoot-mini-mol.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
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/analysis“
Making all in tw
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/tw“
/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.   -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    -DPKGDATADIR='"/usr/share/coot"' -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused  -c -o tw.lo tw.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. -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 -DPKGDATADIR=\"/usr/share/coot\" -O2 -march=core2 -ggdb -pipe -Wall -Wno-unused -c tw.cc  -fPIC -DPIC -o .libs/tw.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-tw.la -rpath /usr/lib64 tw.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/tw.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-tw.so.0 -o .libs/libcoot-tw.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-tw.so.0" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-tw.so" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-tw.la" && ln -s "../libcoot-tw.la" "libcoot-tw.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/tw“
Making all in libgtkgraph
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/libgtkgraph“
/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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o annotation.lo annotation.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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o polar_util.lo polar_util.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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o trace.lo trace.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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o axis.lo axis.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c annotation.c  -fPIC -DPIC -o .libs/annotation.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c trace.c  -fPIC -DPIC -o .libs/trace.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c axis.c  -fPIC -DPIC -o .libs/axis.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c polar_util.c  -fPIC -DPIC -o .libs/polar_util.o
/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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o gtkgraph.lo gtkgraph.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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o polar.lo polar.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.  -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused  -c -o smith.lo smith.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c gtkgraph.c  -fPIC -DPIC -o .libs/gtkgraph.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c polar.c  -fPIC -DPIC -o .libs/polar.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. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -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 -Wunused -c smith.c  -fPIC -DPIC -o .libs/smith.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-gtkgraph.la -rpath /usr/lib64 annotation.lo polar_util.lo trace.lo axis.lo gtkgraph.lo polar.lo smith.lo -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 -lm 
libtool: link: x86_64-pc-linux-gnu-gcc -shared  -fPIC -DPIC  .libs/annotation.o .libs/polar_util.o .libs/trace.o .libs/axis.o .libs/gtkgraph.o .libs/polar.o .libs/smith.o   -Wl,--as-needed -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 -lm  -O2 -march=core2 -ggdb -Wl,-O1   -Wl,-soname -Wl,libcoot-gtkgraph.so.0 -o .libs/libcoot-gtkgraph.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so.0" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so")
libtool: link: ( cd ".libs" && rm -f "libcoot-gtkgraph.la" && ln -s "../libcoot-gtkgraph.la" "libcoot-gtkgraph.la" )
make[1]: Opouští se adresář „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/libgtkgraph“
Making all in lbg
make[1]: Vstupuje se do adresáře „/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2/lbg“
/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.lo lbg.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 wmolecule.lo wmolecule.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 lbg-search.lo lbg-search.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 residue-circles.lo residue-circles.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-search.cc  -fPIC -DPIC -o .libs/lbg-search.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.. -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.cc  -fPIC -DPIC -o .libs/lbg.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.. -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 wmolecule.cc  -fPIC -DPIC -o .libs/wmolecule.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.. -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 residue-circles.cc  -fPIC -DPIC -o .libs/residue-circles.o
residue-circles.cc: In constructor ‘lbg_info_t::optimise_residue_circles::optimise_residue_circles(const std::vector<lbg_info_t::residue_circle_t>&, const std::vector<lbg_info_t::residue_circle_t>&, const widgeted_molecule_t&, const std::vector<int>&)’:
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<unsigned int> lig_build::molecule_t<Ta, Tb>::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<int> lig_build::molecule_t<Ta, Tb>::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<Ta, Tb>::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<bool, std::vector<int> > lig_build::molecule_t<Ta, Tb>::find_bonded_atoms_with_no_pass(int, int, int, const std::vector<int>&, int) const [with Ta = widgeted_atom_t; Tb = widgeted_bond_t]’:
../lidia-core/lig-build.hh:713:25:   required from ‘std::pair<bool, std::vector<int> > lig_build::molecule_t<Ta, Tb>::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<Ta, Tb>::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<unsigned int> lig_build::molecule_t<Ta, Tb>::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<int> lig_build::molecule_t<Ta, Tb>::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<float>&, clipper::Xmap<int>&, clipper::Xmap<int>&, const clipper::Xmap<float>&, const std::vector<clipper::RTop_orth>&) 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<float>&, 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<float>&, 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<double, std::pair<int, int> > Ca_sequence::sequence_score(const std::vector<std::vector<double> >&, 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::CoordList<5> > 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<clipper::String> Ca_sequence::sequence_match(const std::vector<std::vector<double> >&, 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::CoordList<8> > 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<std::basic_string<char>, double> Coot_sequence::sequence_chain(const clipper::Xmap<float>&, const std::vector<std::pair<std::basic_string<char>, std::basic_string<char> > >&, 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<int, int> 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<float>&, const std::vector<LLK_map_target>&, 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<T>::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<T>::add(const ftype&, const T&) [with T = std::pair<int, int>; 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<T>::addable(const ftype&) const [with T = clipper::String; clipper::ftype = double]’:
buccaneer-lib.h:31:23:   required from ‘void Score_list<T>::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<T>::addable(const ftype&) const [with T = std::pair<int, int>; clipper::ftype = double]’:
buccaneer-lib.h:31:23:   required from ‘void Score_list<T>::add(const ftype&, const T&) [with T = std::pair<int, int>; 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<float>&, 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<SearchResult> SSfind::search(const std::vector<std::pair<clipper::Coord_orth, clipper::Coord_orth> >&, const std::vector<clipper::RTop_orth>&, 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>&, 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<int> NucleicAcidJoin::best_chain(std::vector<NucleicAcidJoin::Node>&)’:
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<float>&, 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<float>&, 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<float>&, 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<float>&, 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\" -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 git-revision-count.o git-revision-count.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 c-inner-main.o c-inner-main.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 c-interface-analysis.o c-interface-analysis.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-build.o c-interface-build.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-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 -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-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 -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-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 -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-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    -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-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 -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-mmdb.o c-interface-mmdb.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-mogul.o c-interface-mogul.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-mogul-scripting.o c-interface-mogul-scripting.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-mutate.o c-interface-mutate.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-ncs.o c-interface-ncs.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-network.o c-interface-network.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-nucleotides.o c-interface-nucleotides.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-python.o c-interface-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 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 -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-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; i<g.preferences_internal.size(); i++) {
                   ^
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-refine.o c-interface-refine.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-residues.o c-interface-residues.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-refmac.o c-interface-refmac.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-scm.o c-interface-scm.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-sequence.o c-interface-sequence.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-sfs.o c-interface-sfs.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-superpose.o c-interface-superpose.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-validate.o c-interface-validate.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-view.o c-interface-view.cc
c-interface-validate.cc: In function ‘void gln_asn_b_factor_outliers(int)’:
c-interface-validate.cc:1889:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int i=0; i<v.size(); i++) {
                            ^
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-widgets.o c-interface-widgets.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-waters.o c-interface-waters.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-waters-gui.o c-interface-waters-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.o c-interface.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-test.o c-interface-test.cc
In file included from /usr/include/python2.7/Python.h:80:0,
                 from c-interface.cc:30:
c-interface.cc: In function ‘PyObject* py_residue(const coot::residue_spec_t&)’:
/usr/include/python2.7/object.h:769:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_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 -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 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 -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 cmtz-interface.o cmtz-interface.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 command-line.o command-line.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 command-line-extern.o command-line-extern.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-colour.o coot-colour.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-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 <libguile.h>
                      ^
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
 [31;01m*[0m ERROR: sci-chemistry/coot-0.8.2-r1::gentoo failed (compile phase):
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-chemistry/coot-0.8.2-r1::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-chemistry/coot-0.8.2-r1::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2'
 [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/coot-0.8.2-r1/work/coot-0.8.2'