* Package: sci-chemistry/openbabel-python-2.3.2  * Repository: gentoo  * Maintainer: sci-chemistry@gentoo.org  * USE: abi_ppc_32 elibc_glibc kernel_linux ppc python_targets_python2_7 python_targets_python3_4 userland_GNU  * FEATURES: ccache preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking openbabel-2.3.2.tar.gz to /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 ... * Applying openbabel-python-2.3.2-testpybel.patch ...  [ ok ] * Applying openbabel-python-2.3.2-bindings_only.patch ...  [ ok ] * Applying openbabel-python-2.3.2-swig-3.0.3.patch ...  [ ok ] /usr/include/openbabel-2.0/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored) >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 ... * It seems that you need to set USE_PYTHON to make sure that legacy * packages will be built with respect to PYTHON_TARGETS correctly: * * USE_PYTHON='2.7' * * Please note that after changing the USE_PYTHON variable, you may need * to run 'python-updater' to rebuild affected packages. * * For more information on PYTHON_TARGETS and python.eclass * compatibility, please see the relevant Wiki article [1]. * * [1] https://wiki.gentoo.org/wiki/Project:Python/PYTHON_TARGETS * python3_4: running my_impl_src_configure >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH= -DBINDINGS_ONLY=ON -DBABEL_SYSTEM_LIBRARY=/usr/lib/libopenbabel.so -DOB_MODULE_PATH=/usr/lib/openbabel/2.3.2 -DLIB_INSTALL_DIR=/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/image//usr/lib/python3.4/site-packages -DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python3.4 -DPYTHON_INCLUDE_DIR=/usr/include/python3.4 -DPYTHON_LIBRARY=/usr/lib/libpython3.4.so -DENABLE_TESTS=ON -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/gentoo_common_config.cmake -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -- Check for working C compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -- Check for working CXX compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Using included inchi library. -- Found LibXml2: /usr/lib/libxml2.so (found version "2.9.2") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Found wxWidgets: TRUE -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - not found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found PkgConfig: /usr/bin/powerpc-unknown-linux-gnu-pkg-config (found version "0.28") -- checking for module 'cairo' -- found cairo, version 1.12.18 -- Found Cairo: /usr/lib/libcairo.so -- Cairo found. PNG output will be supported. -- Looking for getopt -- Looking for getopt - found -- Attempting to build the GUI -- wxWidgets found => GUI will be built CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:14 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:31 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:25 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:39 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3.4 (found version "3.4.1") -- Found PythonLibs: /usr/lib/libpython3.4.so -- Python bindings will be compiled -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector C++ -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -pthread Linker flags: Executable -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed Module -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed Shared -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4 * python2_7: running my_impl_src_configure >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python2_7" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python2_7/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH= -DBINDINGS_ONLY=ON -DBABEL_SYSTEM_LIBRARY=/usr/lib/libopenbabel.so -DOB_MODULE_PATH=/usr/lib/openbabel/2.3.2 -DLIB_INSTALL_DIR=/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/image//usr/lib/python2.7/site-packages -DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python2.7 -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/libpython2.7.so -DENABLE_TESTS=ON -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python2_7/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python2_7/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python2_7/gentoo_common_config.cmake -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -- Check for working C compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -- Check for working CXX compiler: /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Using included inchi library. -- Found LibXml2: /usr/lib/libxml2.so (found version "2.9.2") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Found wxWidgets: TRUE -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - not found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found PkgConfig: /usr/bin/powerpc-unknown-linux-gnu-pkg-config (found version "0.28") -- checking for module 'cairo' -- found cairo, version 1.12.18 -- Found Cairo: /usr/lib/libcairo.so -- Cairo found. PNG output will be supported. -- Looking for getopt -- Looking for getopt - found -- Attempting to build the GUI -- wxWidgets found => GUI will be built CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:14 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:54:31 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:25 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at test/CMakeLists.txt:176 (include): Syntax Warning in cmake code at /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:39 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.9") -- Found PythonLibs: /usr/lib/libpython2.7.so (found version "2.7.9") -- Python bindings will be compiled -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector C++ -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -pthread Linker flags: Executable -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed Module -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed Shared -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python2_7 >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 ... * python3_4: running cmake-utils_src_make bindings_python >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4" make -j33 VERBOSE=1 bindings_python /usr/bin/cmake -H/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 -B/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 bindings_python make[1]: Entering directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' /usr/bin/cmake -H/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 -B/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/CMakeFiles 1 make -f CMakeFiles/Makefile2 scripts/CMakeFiles/bindings_python.dir/all make[2]: Entering directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' make -f scripts/CMakeFiles/bindings_python.dir/build.make scripts/CMakeFiles/bindings_python.dir/depend make[3]: Entering directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' cd /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2 /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/scripts /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4 /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts/CMakeFiles/bindings_python.dir/DependInfo.cmake --color= Dependee "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts/CMakeFiles/bindings_python.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts/CMakeFiles/bindings_python.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts/CMakeFiles/bindings_python.dir/depend.internal". Scanning dependencies of target bindings_python make[3]: Leaving directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' make -f scripts/CMakeFiles/bindings_python.dir/build.make scripts/CMakeFiles/bindings_python.dir/build make[3]: Entering directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/CMakeFiles 5 [100%] Building CXX object scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o cd /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/scripts && /usr/lib/ccache/bin/powerpc-unknown-linux-gnu-g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D__WXGTK__ -Dbindings_python_EXPORTS -DNDEBUG -O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector -pthread -fPIC -isystem /usr/lib/wx/include/gtk2-unicode-release-2.8 -isystem /usr/include/wx-2.8 -I/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4/include -I/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/data -I/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/include -I/usr/include/eigen3 -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -o CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o -c /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/scripts/python/openbabel-python.cpp /var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2/scripts/python/openbabel-python.cpp:150:20: fatal error: Python.h: No such file or directory #include ^ compilation terminated. scripts/CMakeFiles/bindings_python.dir/build.make:57: recipe for target 'scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o' failed make[3]: *** [scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o] Error 1 make[3]: Leaving directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' CMakeFiles/Makefile2:7801: recipe for target 'scripts/CMakeFiles/bindings_python.dir/all' failed make[2]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' CMakeFiles/Makefile2:7813: recipe for target 'scripts/CMakeFiles/bindings_python.dir/rule' failed make[1]: *** [scripts/CMakeFiles/bindings_python.dir/rule] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' Makefile:2851: recipe for target 'bindings_python' failed make: *** [bindings_python] Error 2 * ERROR: sci-chemistry/openbabel-python-2.3.2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/openbabel-python-2.3.2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-python-2.3.2::gentoo'`. * The complete build log is located at '/var/log/portage/build/sci-chemistry/openbabel-python-2.3.2:20150426-140547.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2-python3_4' * S: '/var/tmp/portage/sci-chemistry/openbabel-python-2.3.2/work/openbabel-2.3.2'