* Package: sci-libs/avogadrolibs-1.93.0 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc hdf5 kernel_linux qt5 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking avogadrolibs-1.93.0.tar.gz to /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work >>> Source unpacked in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work >>> Preparing source in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 ... * Applying avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch ... [ ok ] * Applying avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build" cmake -C /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/avogadrolibs-1.93.0 -DUSE_PROTOCALL=OFF -DBUILD_GPL_PLUGINS=ON -DUSE_MOLEQUEUE=ON -DUSE_MMTF=OFF -DUSE_LIBMSYM=OFF -DUSE_SPGLIB=OFF -DUSE_PYTHON=OFF -DUSE_LIBARCHIVE=no -DBUILD_DOCUMENTATION=no -DUSE_HDF5=yes -DENABLE_TRANSLATIONS=yes -DUSE_OPENGL=yes -DUSE_QT=yes -DBUILD_STATIC_PLUGINS=ON -DENABLE_TESTING=no -DUSE_VTK=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/gentoo_toolchain.cmake /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 loading initial cache file /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/gentoo_common_config.cmake -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_GCC_ERROR_RETURN_TYPE -- Performing Test HAVE_GCC_ERROR_RETURN_TYPE - Success -- Found Git: /usr/bin/git (found version "2.33.0") -- Could not use git to determine source version, using version 1.93.0 -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found HDF5: hdf5-shared (found version "1.12.1") found components: C CMake Warning (dev) at /usr/share/cmake/Modules/FindOpenGL.cmake:315 (message): Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when available. Run "cmake --help-policy CMP0072" for policy details. Use the cmake_policy command to set the policy and suppress this warning. FindOpenGL found both a legacy GL library: OPENGL_gl_LIBRARY: /usr/lib64/libGL.so and GLVND libraries for OpenGL and GLX: OPENGL_opengl_LIBRARY: /usr/lib64/libOpenGL.so OPENGL_glx_LIBRARY: /usr/lib64/libGLX.so OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for compatibility with CMake 3.10 and below the legacy GL library will be used. Call Stack (most recent call first): avogadro/rendering/CMakeLists.txt:6 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenGL: /usr/lib64/libOpenGL.so -- Found GLEW: /usr/include -- Found PythonInterp: /usr/bin/python (found suitable version "3.9.6", minimum required is "2") Avogadro Generators not found at /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/../avogadrogenerators! CMake Warning (dev) at /usr/share/cmake/Modules/FindOpenGL.cmake:315 (message): Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when available. Run "cmake --help-policy CMP0072" for policy details. Use the cmake_policy command to set the policy and suppress this warning. FindOpenGL found both a legacy GL library: OPENGL_gl_LIBRARY: /usr/lib64/libGL.so and GLVND libraries for OpenGL and GLX: OPENGL_opengl_LIBRARY: /usr/lib64/libOpenGL.so OPENGL_glx_LIBRARY: /usr/lib64/libGLX.so OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for compatibility with CMake 3.10 and below the legacy GL library will be used. Call Stack (most recent call first): avogadro/qtplugins/overlayaxes/CMakeLists.txt:3 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -pipe -march=native -fno-diagnostics-color -O2 C++ -pipe -march=native -fno-diagnostics-color -O2 Linker flags: Executable -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build" ninja -v -j4 -l0 [1/463] 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-I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -isystem /usr/include/eigen3 -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/crystaltools.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/crystaltools.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/crystaltools.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/crystaltools.cpp [16/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 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-I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/cjsonformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/cjsonformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/cjsonformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/cjsonformat.cpp [43/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS 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-I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp FAILED: avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp: In member function ‘bool Avogadro::Io::Hdf5DataFormat::datasetExists(const string&) const’: /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:270:26: error: too few arguments to function ‘herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)’ 270 | if (H5Oget_info_by_name(d->fileId, path.c_str(), &info, H5P_DEFAULT) < 0) | ^ In file included from /usr/include/H5Apublic.h:22, from /usr/include/hdf5.h:23, from /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:19: /usr/include/H5Opublic.h:557:15: note: declared here 557 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields, | ^~~~~~~~~~~~~~~~~~~~ /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp: In member function ‘std::vector > Avogadro::Io::Hdf5DataFormat::datasets() const’: /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:506:25: error: too few arguments to function ‘herr_t H5Ovisit3(hid_t, H5_index_t, H5_iter_order_t, H5O_iterate2_t, void*, unsigned int)’ 506 | herr_t code = H5Ovisit(d->fileId, H5_INDEX_NAME, H5_ITER_INC, | ^ In file included from /usr/include/H5Apublic.h:22, from /usr/include/hdf5.h:23, from /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:19: /usr/include/H5Opublic.h:1326:15: note: declared here 1326 | H5_DLL herr_t H5Ovisit3(hid_t obj_id, H5_index_t idx_type, H5_iter_order_t order, H5O_iterate2_t op, | ^~~~~~~~~ [46/463] 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avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/trrformat.cpp [47/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/xyzformat.cpp [48/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/lammpsformat.cpp ninja: build stopped: subcommand failed. * ERROR: sci-libs/avogadrolibs-1.93.0::gentoo failed (compile phase): * ninja -v -j4 -l0 failed * * Call stack: * ebuild.sh, line 127: Called src_compile * environment, line 2167: Called cmake-utils_src_compile * environment, line 855: Called cmake-utils_src_make * environment, line 1039: Called _cmake_ninja_src_make * environment, line 502: Called eninja * environment, line 1345: Called die * The specific snippet of code: * "$@" || die "${nonfatal_args[@]}" "${*} failed" * * If you need support, post the output of `emerge --info '=sci-libs/avogadrolibs-1.93.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/avogadrolibs-1.93.0::gentoo'`. * The complete build log is located at '/var/log/portage/sci-libs:avogadrolibs-1.93.0:20210826-170820.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build' * S: '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0'