* Package: sci-chemistry/openbabel-python-2.4.1-r1 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_6 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking openbabel-2.4.1.tar.gz to /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1 ... * Applying openbabel-python-2.3.2-gcc-6_and_7-backport.patch ... [ ok ] /usr/include/openbabel-2.0/openbabel/obconversion.h:369: Warning 325: Nested struct not currently supported (StreamState ignored) /usr/include/openbabel-2.0/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored) /usr/include/openbabel-2.0/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored). /usr/include/openbabel-2.0/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored). >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1 ... * python2_7: running my_impl_src_configure >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7" cmake -C /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH= -DBINDINGS_ONLY=ON -DBABEL_SYSTEM_LIBRARY=/usr/lib64/libopenbabel.so -DOB_MODULE_PATH=/usr/lib64/openbabel/2.4.1 -DLIB_INSTALL_DIR=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/image//usr/lib64/python2.7/site-packages -DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python2.7 -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_INCLUDE_PATH=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib64/libpython2.7.so -DENABLE_TESTS=ON -DCMAKE_INSTALL_PREFIX=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/image/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1 loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_common_config.cmake -- The C compiler identification is GNU 8.2.0 -- The CXX compiler identification is GNU 8.2.0 -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_policy): The OLD behavior for policy CMP0005 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at CMakeLists.txt:18 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Using included inchi library. -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.8") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Found wxWidgets: -L/usr/lib64;-pthread;;;-lwx_baseu-3.0;-lwx_gtk2u_core-3.0;-lwx_gtk2u_adv-3.0 (found version "3.0.4") -- 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 - not 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 CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH): MATH cannot parse the expression: "x86_648*10000 + x86_642*100 + x86_640": syntax error, unexpected exp_NUMBER, expecting $end (8) Call Stack (most recent call first): cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION) CMakeLists.txt:248 (macro_ensure_version) CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH): MATH cannot parse the expression: "x86_648*10000 + x86_642*100 + x86_640": syntax error, unexpected exp_NUMBER, expecting $end (8) Call Stack (most recent call first): cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION) CMakeLists.txt:249 (macro_ensure_version) CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH): MATH cannot parse the expression: "x86_648*10000 + x86_642*100 + x86_640": syntax error, unexpected exp_NUMBER, expecting $end (8) Call Stack (most recent call first): cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION) CMakeLists.txt:250 (macro_ensure_version) -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Checking available shared pointer... -- Performing Test HAVE_STD_SHARED_PTR -- Performing Test HAVE_STD_SHARED_PTR - Success -- Performing Test HAVE_STD_TR1_SHARED_PTR -- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success -- Use std::shared_ptr in memory -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "0.29.2") -- Checking for module 'cairo' -- Found cairo, version 1.14.12 -- 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 -- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.15") -- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.15") -- Python bindings will be compiled -- <<< Gentoo configuration >>> Build type Gentoo Install path /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/image/usr Compiler flags: C -O2 -pipe -march=native C++ -O2 -pipe -march=native -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 incomplete, errors occurred! See also "/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/CMakeFiles/CMakeOutput.log". See also "/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/CMakeFiles/CMakeError.log". * ERROR: sci-chemistry/openbabel-python-2.4.1-r1::gentoo failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 124: Called src_configure * environment, line 3964: Called python_foreach_impl 'my_impl_src_configure' * environment, line 3428: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'my_impl_src_configure' * environment, line 2606: Called _multibuild_run '_python_multibuild_wrapper' 'my_impl_src_configure' * environment, line 2604: Called _python_multibuild_wrapper 'my_impl_src_configure' * environment, line 706: Called my_impl_src_configure * environment, line 3962: Called cmake-utils_src_configure * environment, line 1079: Called die * The specific snippet of code: * "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed"; * * If you need support, post the output of `emerge --info '=sci-chemistry/openbabel-python-2.4.1-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-python-2.4.1-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:openbabel-python-2.4.1-r1:20180824-175001.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7' * S: '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1'