sci-libs:votca-tools-1.5:20190406-041041.log

sci-libs:votca-tools-1.5:20190406-041041.log (text/plain), 29.96 KB, created by Toralf Förster on 2019-04-06 07:21:13 UTC

 * Package:    sci-libs/votca-tools-1.5
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * 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
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[27/41] /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/property.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/property.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/property.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/property.cc
[28/41] /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/propertyiomanipulator.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/propertyiomanipulator.cc
[29/41] /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/random2.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/random2.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/random2.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/random2.cc
[30/41] /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/rangeparser.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/rangeparser.cc
[31/41] /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/spline.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/spline.cc
[32/41] /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/table.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/table.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/table.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/table.cc
[33/41] /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/thread.cc.o -MF src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o.d -o src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o -c /var/tmp/portage/sci-libs/votca-tools-1.5/work/tools-1.5/src/libtools/thread.cc
[34/41] /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/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'