* Package: sci-chemistry/openbabel-perl-2.4.1 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux 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-perl-2.4.1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-2.4.1 ... * Applying openbabel-perl-2.3.2-gcc-6_and_7-backport.patch ... [ ok ] * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_BUILD_TYPE RelWithDebInfo) >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-2.4.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build" cmake -C /var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build/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/2.4.1 -DLIB_INSTALL_DIR=/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/image///usr/lib/perl5/vendor_perl/5.30.1/x86_64-linux -DPERL_BINDINGS=ON -DRUN_SWIG=ON -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-2.4.1 loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build/gentoo_common_config.cmake -- The C compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-gcc -- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-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-gentoo-linux-musl-g++ -- Check for working CXX compiler: /usr/bin/x86_64-gentoo-linux-musl-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/lib/libxml2.so (found version "2.9.9") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES wxWidgets_INCLUDE_DIRS) -- 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 - 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_649*10000 + x86_643*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_649*10000 + x86_643*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_649*10000 + x86_643*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-gentoo-linux-musl-pkg-config (found version "1.6.3") -- Checking for module 'cairo' -- Found cairo, version 1.16.0 -- 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 not found => GUI will not be built -- Found PythonInterp: /usr/bin/python (found version "3.8.2") -- Found SWIG: /usr/bin/swig (found version "4.0.0") -- Found SWIG: /usr/bin/swig (found suitable version "4.0.0", minimum required is "2.0") CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (Perl) does not match the name of the calling package (PerlLibs). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): /usr/share/cmake/Modules/FindPerl.cmake:76 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) /usr/share/cmake/Modules/FindPerlLibs.cmake:48 (include) scripts/CMakeLists.txt:295 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Perl: /usr/bin/perl (found version "5.30.1") -- Found PerlLibs: /usr/lib/libperl.so.5.30.1 (found version "5.30.1") -- Perl bindings will be compiled -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=native C++ -O2 -pipe -march=native 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 -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -- Configuring incomplete, errors occurred! See also "/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build/CMakeFiles/CMakeOutput.log". See also "/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build/CMakeFiles/CMakeError.log". * ERROR: sci-chemistry/openbabel-perl-2.4.1::gentoo failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 125: Called src_configure * environment, line 3298: Called cmake-utils_src_configure * environment, line 882: 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-perl-2.4.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-perl-2.4.1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:openbabel-perl-2.4.1:20200404-171528.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-perl-2.4.1_build' * S: '/var/tmp/portage/sci-chemistry/openbabel-perl-2.4.1/work/openbabel-2.4.1'