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Gentoo's Bugzilla – Attachment 445322 Details for
Bug 593310
sci-libs/shogun-4.1.0 - CMake Error: The following variables are used in this project, but they are set to NOTFOUND. - HDF5_hdf5_cpp_LIBRARY
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build.log
build.log (text/x-log), 14.04 KB, created by
Juergen Rose
on 2016-09-09 19:08:58 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Juergen Rose
Created:
2016-09-09 19:08:58 UTC
Size:
14.04 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-libs/shogun-4.1.0 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: sci@gentoo.org >[32;01m * [39;49;00mUSE: abi_x86_64 amd64 elibc_glibc examples kernel_linux lua python python_single_target_python2_7 python_targets_python2_7 python_targets_python3_4 userland_GNU >[32;01m * [39;49;00mFEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking shogun-4.1.0.tar.bz2 to /var/tmp/portage/sci-libs/shogun-4.1.0/work >>>> Unpacking shogun-data-0.9.tar.bz2 to /var/tmp/portage/sci-libs/shogun-4.1.0/work >>>> Source unpacked in /var/tmp/portage/sci-libs/shogun-4.1.0/work >>>> Preparing source in /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0 ... > [32;01m*[0m Applying shogun-4.1.0-fix-buildsystem.patch ... >[A[338C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying shogun-4.1.0-remove-C-linkage.patch ... >[A[338C [34;01m[ [32;01mok[34;01m ][0m >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0 ... >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build" >cmake -C /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_SKIP_INSTALL_RPATH=ON -DCMAKE_SKIP_RPATH=ON -DBUNDLE_ARPREC=OFF -DBUNDLE_COLPACK=OFF -DBUNDLE_EIGEN=OFF -DBUNDLE_JSON=OFF -DBUNDLE_NLOPT=OFF -DENABLE_COVERAGE=OFF -DJavaModular=OFF -DPerlModular=OFF -DLIB_INSTALL_DIR=lib64 -DLuaModular=yes -DCSharpModular=no -DOctaveModular=no -DOctaveStatic=no -DPythonModular=yes -DPythonStatic=yes -DRModular=no -DRStatic=no -DRubyModular=no -DENABLE_TESTING=no -DBUILD_EXAMPLES=yes -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/gentoo_toolchain.cmake /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0 >loading initial cache file /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/gentoo_common_config.cmake >Re-run cmake no build system arguments >-- The C compiler identification is GNU 5.4.0 >-- The CXX compiler identification is GNU 5.4.0 >-- 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 >-- Could NOT find CCache (missing: CCACHE) >-- Found SWIG: /usr/bin/swig (found suitable version "3.0.10", minimum required is "2.0.4") >-- 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 >-- Looking for xmmintrin.h - found >-- Looking for emmintrin.h >-- Looking for emmintrin.h - found >-- Looking for arc4random >-- Looking for arc4random - not found >-- Found GDB: /usr/bin/gdb >-- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR MOSEK_LIBRARY) >-- Looking for pthread.h >-- Looking for pthread.h - found >-- Looking for pthread_create >-- Looking for pthread_create - not found >-- 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 >-- Try OpenMP C flag = [-fopenmp] >-- Performing Test OpenMP_FLAG_DETECTED >-- Performing Test OpenMP_FLAG_DETECTED - Success >-- Try OpenMP CXX flag = [-fopenmp] >-- Performing Test OpenMP_FLAG_DETECTED >-- Performing Test OpenMP_FLAG_DETECTED - Success >-- Found OpenMP: -fopenmp >-- Found PkgConfig: /usr/bin/x86_64-pc-linux-gnu-pkg-config (found version "0.29.1") >-- Checking for module 'lapack' >-- Found lapack, version 3.11.38 >-- Found LAPACK: /usr/lib64/libatllapack.so;/usr/lib64/libf77blas.so;/usr/lib64/libatlcblas.so >-- Looking for clapack_dpotrf in >-- Looking for clapack_dpotrf in - not found >-- Could NOT find ATLAS (missing: ATLAS_LIBRARIES) >-- Found CBLAS: /usr/lib64/libgslcblas.so >-- Looking for cblas_dsyrk in /usr/lib64/libgslcblas.so >-- Looking for cblas_dsyrk in /usr/lib64/libgslcblas.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 "3.2.8", minimum required is "3.1.2") >-- Found OPENCL: /usr/lib64/libOpenCL.so >-- Could NOT find ViennaCL (missing: VIENNACL_INCLUDE_DIR) (Required is at least version "1.5.0") >-- Checking for one of the modules 'libColPack>=1.0.9;ColPack>=1.0.9' >-- Found NLOPT: /usr/lib64/libnlopt.so >-- Found LPSOLVE: /usr/lib64/liblpsolve55.so >-- Found ColPack: /usr/lib64/libColPack.so >-- Found ARPREC: /usr/lib64/libarprec.so >-- Found Doxygen: /usr/bin/doxygen (found suitable version "1.8.11", minimum required is "1.8.6") >-- Found PythonInterp: /var/tmp/portage/sci-libs/shogun-4.1.0/temp/python2.7/bin/python (found version "2.7.12") >-- Checking for one of the modules 'libjson>=0.11;json>=0.11;json-c>=0.11' >-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.4") >-- HDF5: Using hdf5 compiler wrapper to determine C configuration >-- Found HDF5: /usr/lib64/libsz.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;HDF5_hdf5_cpp_LIBRARY-NOTFOUND;/usr/lib64/libhdf5.so (found version "1.8.15.1") >-- Found CURL: /usr/lib64/libcurl.so (found version "7.50.2") >-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.8") >-- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6") >-- Looking for BZ2_bzCompressInit >-- Looking for BZ2_bzCompressInit - found >-- Looking for lzma_auto_decoder in /usr/lib64/liblzma.so >-- Looking for lzma_auto_decoder in /usr/lib64/liblzma.so - found >-- Looking for lzma_easy_encoder in /usr/lib64/liblzma.so >-- Looking for lzma_easy_encoder in /usr/lib64/liblzma.so - found >-- Looking for lzma_lzma_preset in /usr/lib64/liblzma.so >-- Looking for lzma_lzma_preset in /usr/lib64/liblzma.so - found >-- Found LibLZMA: /usr/include (found version "5.2.2") >-- Found SNAPPY: /usr/lib64/libsnappy.so >-- Lzo Library /usr/lib64/liblzo2.so >-- Lzo Include Found in /usr/include >-- Spinlock support found >-- Found Protobuf: /usr/lib64/libprotobuf.so;-lpthread (found version "3.0.0") >-- Supported backend(s) for linear algebra FOUND and ENABLED >-- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.12") >-- Found NumPy: version "1.11.1" /usr/lib64/python2.7/site-packages/numpy/core/include >-- Checking for one of the modules 'lua;lua5.1' >-- =================================================================================================================== >-- Summary of Configuration Variables >-- >-- The following OPTIONAL packages have been found: > > * GDB > * OpenMP > * LAPACK > * CBLAS > * GLPK > * ARPACK > * Eigen3 (required version >= 3.1.2) > * NLopt > * LpSolve > * ColPack > * ARPREC > * Doxygen (required version >= 1.8.6) > * LibXml2 > * HDF5 > * CURL > * ZLIB > * BZip2 > * LibLZMA > * SNAPPY > * LZO > * Spinlock > * Threads > * Protobuf > >-- The following REQUIRED packages have been found: > > * SWIG (required version >= 2.0.4) > * OpenCL > * PkgConfig > * PythonLibs > * PythonInterp > * NumPy > >-- The following OPTIONAL packages have not been found: > > * CCache > * Mosek > * Atlas > * CPLEX > * ViennaCL (required version >= 1.5.0) > >-- =================================================================================================================== >-- Enabled Integration >-- OpenCV Integration is OFF - enable with -DOpenCV=ON >-- =================================================================================================================== >-- Enabled Interfaces >-- libshogun is ON >-- python modular is ON >-- octave modular is OFF - enable with -DOctaveModular=ON >-- java modular is OFF - enable with -DJavaModular=ON >-- perl modular is OFF - enable with -DPerlModular=ON >-- ruby modular is OFF - enable with -DRubyModular=ON >-- csharp modular is OFF - enable with -DCSharpModular=ON >-- R modular is OFF - enable with -DRModular=ON >-- lua modular is ON >-- >-- Enabled legacy interfaces >-- cmdline static is OFF - enable with -DCmdLineStatic=ON >-- python static is ON >-- octave static is OFF - enable with -DOctaveStatic=ON >-- matlab static is OFF - enable with -DMatlabStatic=ON >-- R static is OFF - enable with -DRStatic=ON >-- =================================================================================================================== >-- To compile shogun type >-- make >-- >-- To install shogun to /usr type >-- make install >-- >-- or to install to a custom directory >-- make install DESTDIR=/my/special/path >-- (or rerun cmake with -DCMAKE_INSTALL_PREFIX=/my/special/path) to just change the prefix >-- =================================================================================================================== >-- <<< Gentoo configuration >>> >Build type Gentoo >Install path /usr >Compiler flags: >C -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -march=native -O2 -pipe -fopenmp >C++ -std=c++11 -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -march=native -O2 -pipe -fopenmp >Linker flags: >Executable -Wl,-O1 -Wl,--as-needed >Module -Wl,-O1 -Wl,--as-needed >Shared -Wl,-O1 -Wl,--as-needed > >CMake Error: The following variables are used in this project, but they are set to NOTFOUND. >Please set them or make sure they are set and tested correctly in the CMake files: >HDF5_hdf5_cpp_LIBRARY > linked by target "shogun" in directory /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0/src/shogun > >-- Configuring incomplete, errors occurred! >See also "/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/CMakeFiles/CMakeOutput.log". >See also "/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/CMakeFiles/CMakeError.log". > [31;01m*[0m ERROR: sci-libs/shogun-4.1.0::gentoo failed (configure phase): > [31;01m*[0m cmake failed > [31;01m*[0m > [31;01m*[0m Call stack: > [31;01m*[0m ebuild.sh, line 115: Called src_configure > [31;01m*[0m environment, line 4124: Called cmake-utils_src_configure > [31;01m*[0m environment, line 1078: Called _cmake_execute_optionally 'src_configure' > [31;01m*[0m environment, line 444: Called enable_cmake-utils_src_configure > [31;01m*[0m environment, line 1510: Called die > [31;01m*[0m The specific snippet of code: > [31;01m*[0m "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed"; > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-libs/shogun-4.1.0::gentoo'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-libs/shogun-4.1.0::gentoo'`. > [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-libs/shogun-4.1.0/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-libs/shogun-4.1.0/temp/environment'. > [31;01m*[0m Working directory: '/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build' > [31;01m*[0m S: '/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0'
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bug 593310
: 445322