* Package: sci-libs/votca-tools-1.5 * Repository: gentoo * Maintainer: junghans@gentoo.org sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc fftw kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... >>> Unpacking votca-tools-1.5.tar.gz to /var/tmp/portage/sci-libs/votca-tools-1.5/work >>> Source unpacked in /var/tmp/portage/sci-libs/votca-tools-1.5/work >>> Preparing source in /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build" cmake -C /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DWITH_FFTW=yes -DWITH_SQLITE3=no -DWITH_RC_FILES=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/gentoo_toolchain.cmake /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5 loading initial cache file /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/gentoo_common_config.cmake -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- 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 -- 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 -- Boost version: 1.67.0 -- Found the following Boost libraries: -- program_options -- filesystem -- system -- Intel(R) MKL could not be found. -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.3.0") -- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "1.5.4") -- Checking for module 'fftw3' -- Found fftw3, version 3.3.8 -- Found FFTW3: /usr/lib64/libfftw3.so -- Looking for fftw_plan_r2r_1d in /usr/lib64/libfftw3.so; -- Looking for fftw_plan_r2r_1d in /usr/lib64/libfftw3.so; - found -- Looking for assert.h -- Looking for assert.h - found -- Looking for math.h -- Looking for math.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for C++ include cmath -- Looking for C++ include cmath - found -- Looking for C++ include fstream -- Looking for C++ include fstream - found -- Looking for C++ include functional -- Looking for C++ include functional - found -- Looking for C++ include iostream -- Looking for C++ include iostream - found -- Looking for C++ include limits -- Looking for C++ include limits - found -- Looking for C++ include list -- Looking for C++ include list - found -- Looking for C++ include map -- Looking for C++ include map - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for C++ include stack -- Looking for C++ include stack - found -- Looking for C++ include stdexcept -- Looking for C++ include stdexcept - found -- Looking for C++ include string -- Looking for C++ include string - found -- Looking for C++ include vector -- Looking for C++ include vector - found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Found EXPAT: /opt/tivoli/tsm/client/ba/bin/libexpat.so (found version "2.2.6") -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- The following OPTIONAL packages have been found: * FFTW3 * PkgConfig * EXPAT -- The following REQUIRED packages have been found: * Threads * Boost (required version >= 1.57.0) * Eigen3 (required version >= 3.3.0) -- The following OPTIONAL packages have not been found: * MKL * Doxygen -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=native C++ -O2 -pipe -march=native Linker flags: Executable -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed Module -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed Shared -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build" ninja -v -j1 -l0 [1/41] cd /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/libtools && /usr/bin/cmake -DTOP_SOURCE_DIR="/var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5" -DGIT_EXECUTABLE="" -DMERCURIAL_EXECUTABLE="" -P /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/CMakeModules/gitversion.cmake [2/41] /usr/bin/x86_64-pc-linux-gnu-g++ -Dvotca_tools_EXPORTS -I/var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/include -Iinclude -I/usr/include/eigen3 -Isrc/libtools -DNDEBUG -O2 -pipe -march=native -fPIC -std=c++11 -MD -MT src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o.d -o 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src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/tokenizer.cc [35/41] /usr/bin/x86_64-pc-linux-gnu-g++ -Dvotca_tools_EXPORTS -I/var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/include -Iinclude -I/usr/include/eigen3 -Isrc/libtools -DNDEBUG -O2 -pipe -march=native -fPIC -std=c++11 -MD -MT src/libtools/CMakeFiles/votca_tools.dir/version.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/version.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/version.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/version.cc [36/41] : && /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -O2 -pipe -march=native -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libvotca_tools.so.5 -o src/libtools/libvotca_tools.so.5 src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o src/libtools/CMakeFiles/votca_tools.dir/application.cc.o src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o src/libtools/CMakeFiles/votca_tools.dir/edge.cc.o src/libtools/CMakeFiles/votca_tools.dir/edgecontainer.cc.o src/libtools/CMakeFiles/votca_tools.dir/elements.cc.o src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o src/libtools/CMakeFiles/votca_tools.dir/graph_bf_visitor.cc.o src/libtools/CMakeFiles/votca_tools.dir/graphalgorithm.cc.o src/libtools/CMakeFiles/votca_tools.dir/graphdistvisitor.cc.o src/libtools/CMakeFiles/votca_tools.dir/graphnode.cc.o src/libtools/CMakeFiles/votca_tools.dir/graphvisitor.cc.o src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o src/libtools/CMakeFiles/votca_tools.dir/matrix.cc.o src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o src/libtools/CMakeFiles/votca_tools.dir/parsexml.cc.o src/libtools/CMakeFiles/votca_tools.dir/property.cc.o src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o src/libtools/CMakeFiles/votca_tools.dir/random2.cc.o src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o src/libtools/CMakeFiles/votca_tools.dir/table.cc.o src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o src/libtools/CMakeFiles/votca_tools.dir/version.cc.o -L/opt/tivoli/tsm/client/ba/bin -Wl,-rpath,/opt/tivoli/tsm/client/ba/bin: -lboost_program_options-mt -lboost_filesystem-mt -lboost_system-mt -lfftw3 -lexpat -lpthread -lm && : [37/41] /usr/bin/cmake -E cmake_symlink_library src/libtools/libvotca_tools.so.5 src/libtools/libvotca_tools.so.5 src/libtools/libvotca_tools.so && : [38/41] /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/include -Iinclude -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=native -std=c++11 -MD -MT src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o -MF src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o.d -o src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/tools/votca_property.cc [39/41] : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed -rdynamic src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o -o src/tools/votca_property -L/opt/tivoli/tsm/client/ba/bin -Wl,-rpath,/var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/libtools:/opt/tivoli/tsm/client/ba/bin: src/libtools/libvotca_tools.so.5 -lboost_program_options-mt -lboost_filesystem-mt -lboost_system-mt -lfftw3 -lexpat -lpthread -lm && : [40/41] cd /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools && /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property --man > votca_property.man FAILED: src/tools/votca_property.man cd /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools && /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property --man > votca_property.man /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/libtools/libvotca_tools.so.5) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/libtools/libvotca_tools.so.5) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib64/libboost_program_options.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/lib64/libboost_program_options.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib64/libboost_program_options.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/lib64/libboost_filesystem.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib64/libboost_filesystem.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/lib64/libboost_filesystem.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib64/libboost_filesystem.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib64/libboost_system.so.1.67.0) /var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build/src/tools/votca_property: /opt/tivoli/tsm/client/ba/bin/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib64/libboost_system.so.1.67.0) ninja: build stopped: subcommand failed. * ERROR: sci-libs/votca-tools-1.5::gentoo failed (compile phase): * ninja -v -j1 -l0 failed * * Call stack: * ebuild.sh, line 124: Called src_compile * environment, line 2774: Called cmake-utils_src_compile * environment, line 696: Called cmake-utils_src_make * environment, line 877: Called _cmake_ninja_src_make * environment, line 375: Called eninja * environment, line 1207: Called die * The specific snippet of code: * "$@" || die "${nonfatal_args[@]}" "${*} failed" * * If you need support, post the output of `emerge --info '=sci-libs/votca-tools-1.5::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/votca-tools-1.5::gentoo'`. * The complete build log is located at '/var/log/portage/sci-libs:votca-tools-1.5:20190406-041041.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/votca-tools-1.5/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/votca-tools-1.5/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/votca-tools-1.5/work/votca-tools-1.5_build' * S: '/var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5'