* Package: sci-libs/shogun-5.0.0-r1 * Repository: gentoo * Maintainer: sci@gentoo.org * USE: abi_x86_64 amd64 cpu_flags_x86_sse elibc_glibc kernel_linux python_single_target_python3_6 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking shogun-5.0.0.tar.bz2 to /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work >>> Source unpacked in /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work >>> Preparing source in /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0 ... * Applying shogun-5.0.0-fix-buildsystem.patch ... [ ok ] * Applying shogun-4.1.0-remove-C-linkage.patch ... patching file src/interfaces/r_modular/sg_print_functions.cpp Hunk #2 succeeded at 6 with fuzz 2. [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_build" cmake -C /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_SKIP_RPATH=ON -DCMAKE_SKIP_INSTALL_RPATH=ON -DLIB_INSTALL_DIR=lib64 -DENABLE_TESTING=no -DBUILD_EXAMPLES=no -DDISABLE_SSE=no -DCMAKE_DISABLE_FIND_PACKAGE_Pandoc=ON -DCMAKE_DISABLE_FIND_PACKAGE_Sphinx=ON -DCMAKE_DISABLE_FIND_PACKAGE_Doxygen=ON -DENABLE_COVERAGE=OFF -DENABLE_COLPACK=ON -DENABLE_PROTOBUF=ON -DENABLE_PYTHON_DEBUG=OFF -DENABLE_VIENNACL=no -DUSE_ARPREC=ON -DUSE_HDF5=ON -DJavaModular=OFF -DPerlModular=OFF -DCSharpModular=OFF -DLuaModular=no -DOctaveModular=no -DPythonModular=no -DRModular=no -DRubyModular=no -DBUNDLE_COLPACK=OFF -DBUNDLE_JSON=OFF -DBUNDLE_NLOPT=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_build/gentoo_toolchain.cmake /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0 loading initial cache file /var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_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-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 -- Found CCache: /usr/bin/ccache -- Performing Test _HAS_CXX11_FLAG -- Performing Test _HAS_CXX11_FLAG - Success -- Checking C++11 support for "__func__" -- Checking C++11 support for "__func__": works -- Checking C++11 support for "atomic" -- Checking C++11 support for "atomic": works -- Checking C++11 support for "auto" -- Checking C++11 support for "auto": works -- Checking C++11 support for "auto_ret_type" -- Checking C++11 support for "auto_ret_type": works -- Checking C++11 support for "class_override_final" -- Checking C++11 support for "class_override_final": not supported -- Checking C++11 support for "constexpr" -- Checking C++11 support for "constexpr": works -- Checking C++11 support for "cstdint" -- Checking C++11 support for "cstdint": works -- Checking C++11 support for "decltype" -- Checking C++11 support for "decltype": works -- Checking C++11 support for "initializer_list" -- Checking C++11 support for "initializer_list": works -- Checking C++11 support for "lambda" -- Checking C++11 support for "lambda": works -- Checking C++11 support for "long_long" -- Checking C++11 support for "long_long": works -- Checking C++11 support for "nullptr" -- Checking C++11 support for "nullptr": works -- Checking C++11 support for "regex" -- Checking C++11 support for "regex": works -- Checking C++11 support for "rvalue-references" -- Checking C++11 support for "rvalue-references": works -- Checking C++11 support for "sizeof_member" -- Checking C++11 support for "sizeof_member": works -- Checking C++11 support for "static_assert" -- Checking C++11 support for "static_assert": works -- Checking C++11 support for "variadic_templates" -- Checking C++11 support for "variadic_templates": works -- Looking for C++ include unordered_map -- Looking for C++ include unordered_map - found -- Using system's malloc -- Looking for isfinite -- Looking for isfinite - not found -- Looking for isinf -- Looking for isinf - not found -- Looking for isnan -- Looking for isnan - not found -- Looking for signgam -- Looking for signgam - found -- Looking for fdopen -- Looking for fdopen - found -- Looking for log2 -- Looking for log2 - found -- Looking for powl -- Looking for powl - found -- Looking for lgammal -- Looking for lgammal - found -- Looking for sqrtl -- Looking for sqrtl - found -- Looking for finite -- Looking for finite - found -- Looking for isfinite -- Looking for isfinite - not found -- Looking for isinf -- Looking for isinf - found -- Looking for isnan -- Looking for isnan - found -- Performing Test HAVE_STD_ISINF -- Performing Test HAVE_STD_ISINF - Success -- Performing Test HAVE_STD_ISFINITE -- Performing Test HAVE_STD_ISFINITE - Success -- Performing Test HAVE_STD_ISNAN -- Performing Test HAVE_STD_ISNAN - Success -- Looking for xmmintrin.h CMake Warning (dev) at /usr/share/cmake/Modules/CheckIncludeFile.cmake:80 (message): Policy CMP0075 is not set: Include file check macros honor CMAKE_REQUIRED_LIBRARIES. Run "cmake --help-policy CMP0075" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMAKE_REQUIRED_LIBRARIES is set to: m For compatibility with CMake 3.11 and below this check is ignoring it. Call Stack (most recent call first): CMakeLists.txt:470 (CHECK_INCLUDE_FILE) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for xmmintrin.h - found -- Looking for emmintrin.h -- Looking for emmintrin.h - found -- Looking for arc4random -- Looking for arc4random - not found -- Could NOT find GDB (missing: GDB_COMMAND GDB_VERSION) CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (MOSEK) does not match the name of the calling package (Mosek). 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): cmake/FindMosek.cmake:515 (find_package_handle_standard_args) CMakeLists.txt:490 (FIND_PACKAGE) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR MOSEK_LIBRARY) -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "1.6.3") -- Checking for module 'lapack' -- Found lapack, version 3.8.0 -- Found LAPACK: /usr/lib64/liblapack.so -- Could NOT find Atlas (missing: Atlas_CLAPACK_INCLUDE_DIR Atlas_BLAS_LIBRARY Atlas_LAPACK_LIBRARY) -- Found CBLAS: /usr/lib64/libcblas.so -- Looking for cblas_dsyrk in /usr/lib64/libcblas.so -- Looking for cblas_dsyrk in /usr/lib64/libcblas.so - found -- Found GLPK: /usr/lib64/libglpk.so -- Could NOT find CPLEX (missing: CPLEX_LIBRARY CPLEX_INCLUDE_DIR) -- Found Arpack : /usr/lib64/libarpack.so -- Found Eigen3: /usr/include/eigen3 (found suitable version "3.3.7", minimum required is "3.1.2") CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (OPENCL) does not match the name of the calling package (OpenCL). 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): cmake/FindOpenCL.cmake:61 (find_package_handle_standard_args) cmake/FindViennaCL.cmake:15 (find_package) CMakeLists.txt:598 (FIND_PACKAGE) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OPENCL: /usr/lib64/libOpenCL.so -- Could NOT find ViennaCL (missing: VIENNACL_INCLUDE_DIR VIENNACL_ENCODED_VERSION) (Required is at least version "1.5.0") -- Checking for one of the modules 'libColPack>=1.0.9;ColPack>=1.0.9' CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (NLOPT) does not match the name of the calling package (NLopt). 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): cmake/FindNLopt.cmake:22 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) CMakeLists.txt:644 (FIND_PACKAGE) This warning is for project developers. Use -Wno-dev to suppress it. -- Found NLOPT: /usr/lib64/libnlopt.so CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (LPSOLVE) does not match the name of the calling package (LpSolve). 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): cmake/FindLpSolve.cmake:23 (find_package_handle_standard_args) CMakeLists.txt:652 (FIND_PACKAGE) This warning is for project developers. Use -Wno-dev to suppress it. -- Found LPSOLVE: /usr/lib64/liblpsolve55.so -- Found ColPack: /usr/lib64/libColPack.so -- Found ARPREC: /usr/lib64/libarprec.so -- Found PythonInterp: /usr/bin/python (found version "3.8.2") CMake Warning at cmake/FindPLY.cmake:24 (message): ply import failure: Call Stack (most recent call first): CMakeLists.txt:698 (FIND_PACKAGE) CMake Error at CMakeLists.txt:700 (message): Python module ply required for meta examples. Disable meta examples or install python-ply -- Configuring incomplete, errors occurred! See also "/var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_build/CMakeFiles/CMakeOutput.log". See also "/var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_build/CMakeFiles/CMakeError.log". * ERROR: sci-libs/shogun-5.0.0-r1::gentoo failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 125: Called src_configure * environment, line 3995: Called cmake-utils_src_configure * environment, line 1356: 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-libs/shogun-5.0.0-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/shogun-5.0.0-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-libs:shogun-5.0.0-r1:20200407-213427.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/shogun-5.0.0-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/shogun-5.0.0-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0_build' * S: '/var/tmp/portage/sci-libs/shogun-5.0.0-r1/work/shogun-5.0.0'