* Package: sci-chemistry/votca-csg-1.4 * Repository: gentoo * Maintainer: junghans@gentoo.org sci-chemistry@gentoo.org * 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 [8/92] /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/boundarycondition.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/boundarycondition.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/boundarycondition.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/boundarycondition.cc [9/92] /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/cgengine.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/cgengine.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/cgengine.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/cgengine.cc [10/92] /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/cgmoleculedef.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/cgmoleculedef.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/cgmoleculedef.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/cgmoleculedef.cc [11/92] /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/csgapplication.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/csgapplication.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/csgapplication.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/csgapplication.cc [12/92] /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/exclusionlist.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/exclusionlist.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/exclusionlist.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/exclusionlist.cc [13/92] /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/imcio.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/imcio.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/imcio.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/imcio.cc [14/92] /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/map.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/map.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/map.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/map.cc [15/92] /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/molecule.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/molecule.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/molecule.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/molecule.cc [16/92] /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/nblist.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/nblist.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/nblist.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/nblist.cc [17/92] /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/nblistgrid.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/nblistgrid.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/nblistgrid.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/nblistgrid.cc [18/92] /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/nematicorder.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/nematicorder.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/nematicorder.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/nematicorder.cc [19/92] /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/openbox.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/openbox.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/openbox.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/openbox.cc [20/92] /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/orthorhombicbox.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/orthorhombicbox.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/orthorhombicbox.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/orthorhombicbox.cc [21/92] /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/potentialfunctions/potentialfunction.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunction.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunction.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/potentialfunctions/potentialfunction.cc [22/92] /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/potentialfunctions/potentialfunctioncbspl.cc.o -MF 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-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/potentialfunctions/potentialfunctionljg.cc.o -MF src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunctionljg.cc.o.d -o src/libcsg/CMakeFiles/votca_csg.dir/potentialfunctions/potentialfunctionljg.cc.o -c /var/tmp/portage/sci-chemistry/votca-csg-1.4/work/csg-1.4/src/libcsg/potentialfunctions/potentialfunctionljg.cc [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'