sci-chemistry:votca-csg-1.4:20190504-031450.log

sci-chemistry:votca-csg-1.4:20190504-031450.log (text/plain), 24.02 KB, created by Toralf Förster on 2019-05-04 08:31:52 UTC

 * Package:    sci-chemistry/votca-csg-1.4
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc gromacs kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking votca-csg-1.4.tar.gz to /var/tmp/portage/sci-chemistry/votca-csg-1.4/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/votca-csg-1.4/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build"
cmake -C /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DWITH_GMX=yes -DWITH_H5MD=no -DWITH_RC_FILES=OFF -DLIB=lib64 -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4
loading initial cache file /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 8.2.0
-- The CXX compiler identification is GNU 8.2.0
-- 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
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
-- 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  
-- Found TXT2TAGS: /usr/bin/txt2tags  
-- Found UnixCommands: /bin/bash  
-- Boost version: 1.65.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "0.29.2") 
-- Checking for module 'libvotca_tools'
--   Found libvotca_tools, version 
-- Found VOTCA_TOOLS: /usr/lib/libvotca_tools.so  
-- Looking for VotcaToolsFromC in /usr/lib/libvotca_tools.so
-- Looking for VotcaToolsFromC in /usr/lib/libvotca_tools.so - found
-- Checking for module 'libgromacs_d'
--   No package 'libgromacs_d' found
-- Checking for module 'libgromacs'
--   Found libgromacs, version 2018.3
-- Looking for GromacsVersion in /usr/lib/libgromacs.so
-- Looking for GromacsVersion in /usr/lib/libgromacs.so - not found
-- Looking for c++ gmx_version in /usr/lib/libgromacs.so
-- Looking for c++ gmx_version in /usr/lib/libgromacs.so - found
-- Looking for init_domdec_vsites in /usr/lib/libgromacs.so
-- Looking for init_domdec_vsites in /usr/lib/libgromacs.so - not found
-- Looking for gmx_gpu_sharing_supported in /usr/lib/libgromacs.so
-- Looking for gmx_gpu_sharing_supported in /usr/lib/libgromacs.so - not found
-- Looking for c++ gmx_is_single_precision in /usr/lib/libgromacs.so
-- Looking for c++ gmx_is_single_precision in /usr/lib/libgromacs.so - found
-- Looking for c++ gmx_is_double_precision in /usr/lib/libgromacs.so
-- Looking for c++ gmx_is_double_precision in /usr/lib/libgromacs.so - not found
-- Found GROMACS: /usr/lib/libgromacs.so  
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - 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 numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - 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 C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.14") found components:  doxygen missing components:  dot
-- The following OPTIONAL packages have been found:

 * TXT2TAGS
 * UnixCommands
 * PkgConfig
 * Doxygen

-- The following REQUIRED packages have been found:

 * Threads
 * Boost (required version >= 1.39.0)
 * VOTCA_TOOLS
 * GROMACS

-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -pipe -march=native
C++             -O2 -pipe -march=native -std=c++11
Linker flags:
Executable      -Wl,-O1 -Wl,--as-needed
Module          -Wl,-O1 -Wl,--as-needed
Shared          -Wl,-O1 -Wl,--as-needed

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build"
ninja -v -j1 -l0
[1/92] cd /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts && /usr/bin/cmake -DINPUT="csg_call.out" -DOUTPUT="csg_call" -DGIT_EXECUTABLE="" -DMERCURIAL_EXECUTABLE="" -DTOP_SOURCE_DIR="/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4" -P /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/CMakeModules/gitscript.cmake
[2/92] cd /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts && /usr/bin/cmake -DINPUT="help2t2t.out" -DOUTPUT="help2t2t" -DGIT_EXECUTABLE="" -DMERCURIAL_EXECUTABLE="" -DTOP_SOURCE_DIR="/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4" -P /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/CMakeModules/gitscript.cmake
[3/92] cd /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts && VOTCASHARE=/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/share /bin/bash /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts/csg_call --help > csg_call.help && /bin/bash /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts/help2t2t csg_call.help > csg_call.t2t && /usr/bin/txt2tags -q -t man -i csg_call.t2t -o csg_call.man
[4/92] cd /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts && /usr/bin/cmake -DINPUT="csg_inverse.out" -DOUTPUT="csg_inverse" -DGIT_EXECUTABLE="" -DMERCURIAL_EXECUTABLE="" -DTOP_SOURCE_DIR="/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4" -P /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/CMakeModules/gitscript.cmake
[5/92] cd /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts && VOTCASHARE=/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/share /bin/bash /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts/csg_inverse --help > csg_inverse.help && /bin/bash /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/scripts/help2t2t csg_inverse.help > csg_inverse.t2t && /usr/bin/txt2tags -q -t man -i csg_inverse.t2t -o csg_inverse.man
[6/92] cd /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build/src/libcsg && /usr/bin/cmake -DTOP_SOURCE_DIR="/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4" -DGIT_EXECUTABLE="" -DMERCURIAL_EXECUTABLE="" -P /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/CMakeModules/gitversion.cmake
[7/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/beadlist.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/beadlist.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/beadlist.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/beadlist.cc
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[25/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/topology.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/topology.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/topology.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/topology.cc
[26/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/topologymap.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/topologymap.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/topologymap.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/topologymap.cc
[27/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/topologyreader.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/topologyreader.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/topologyreader.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/topologyreader.cc
[28/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/trajectoryreader.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/trajectoryreader.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/trajectoryreader.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/trajectoryreader.cc
[29/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/trajectorywriter.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/trajectorywriter.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/trajectorywriter.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/trajectorywriter.cc
[30/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/triclinicbox.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/triclinicbox.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/triclinicbox.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/triclinicbox.cc
[31/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/version.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/version.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/version.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/version.cc
[32/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtopologyreader.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/modules/io/gmxtopologyreader.cc
[33/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectoryreader.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/modules/io/gmxtrajectoryreader.cc
[34/92] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/modules/io/gmxtrajectorywriter.cc
FAILED: src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o 
/usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -Dvotca_csg_EXPORTS -I/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/include -Isrc/libcsg  -DNDEBUG -O2 -pipe -march=native -std=c++11 -fPIC -MD -MT src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/modules/io/gmxtrajectorywriter.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/modules/io/gmxtrajectorywriter.cc
/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/modules/io/gmxtrajectorywriter.cc: In member function ‘virtual void votca::csg::GMXTrajectoryWriter::Write(votca::csg::Topology*)’:
/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/modules/io/gmxtrajectorywriter.cc:51:11: error: ‘t_trxframe’ {aka ‘struct t_trxframe’} has no member named ‘bTitle’; did you mean ‘bTime’?
     frame.bTitle=false;
           ^~~~~~
           bTime
ninja: build stopped: subcommand failed.
 * ERROR: sci-chemistry/votca-csg-1.4::gentoo failed (compile phase):
 *   ninja -v -j1 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  124:  Called src_compile
 *   environment, line 2840:  Called cmake-utils_src_compile
 *   environment, line  718:  Called cmake-utils_src_make
 *   environment, line  899:  Called _cmake_ninja_src_make
 *   environment, line  386:  Called eninja
 *   environment, line 1236:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/votca-csg-1.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/votca-csg-1.4::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:votca-csg-1.4:20190504-031450.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/votca-csg-1.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/votca-csg-1.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/votca-csg-1.4_build'
 * S: '/var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4'