* Package: sci-chemistry/avogadro-1.0.3-r1 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: amd64 elibc_glibc glsl kernel_linux multilib python sse2 userland_GNU * FEATURES: sandbox >>> Unpacking source... >>> Unpacking avogadro-1.0.3.tar.bz2 to /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3 ... * Applying 1.0.1-gl2ps.patch ...  [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/temp/gentoo_common_config.cmake -DCMAKE_INSTALL_PREFIX=/usr -DENABLE_THREADGL=FALSE -DENABLE_RPATH=OFF -DENABLE_UPDATE_CHECKER=OFF -DQT_MKSPECS_DIR=/usr/share/qt4/mkspecs -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs -DENABLE_glsl=ON -DENABLE_GLSL=ON -DENABLE_Glsl=ON -DWITH_SSE2=ON -DENABLE_python=ON -DENABLE_PYTHON=ON -DENABLE_Python=ON -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/temp/gentoo_rules.cmake /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/temp/gentoo_common_config.cmake Re-run cmake no build system arguments -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- 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 -- 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 -- The build type is Gentoo -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Performing Test COMPILES_WITHOUT_FPERMISSIVE -- Performing Test COMPILES_WITHOUT_FPERMISSIVE - Failed -- Enabling the SSE2 instruction set -- Looking for Q_WS_X11 -- Looking for Q_WS_X11 - found -- Looking for Q_WS_WIN -- Looking for Q_WS_WIN - not found. -- Looking for Q_WS_QWS -- Looking for Q_WS_QWS - not found. -- Looking for Q_WS_MAC -- Looking for Q_WS_MAC - not found. -- Found Qt4: /usr/bin/qmake (found suitable version "4.8.0", required is "4.5.1") -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib64/libX11.so -- Found OpenGL: /usr/lib64/libGL.so -- Found lupdate: /usr/bin/lupdate -- Found lrelease: /usr/bin/lrelease -- Found lconvert: /usr/bin/lconvert -- Found Eigen2: /usr/include/eigen2 -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.6") -- checking for module 'openbabel-2.0>=2.2.2' -- found openbabel-2.0, version 2.3.1 -- Found OpenBabel 2.2 or later: openbabel -- Found OpenBabel2 executable: /usr/bin/babel -- Found Git revision is: -- Building released version. -- Searching for python dependencies... -- [1/5] Boost Python -- Boost version: 1.48.0 -- Found the following Boost libraries: -- python -- Boost Python found... -- [2/5] Python Libraries -- Found PythonLibs: /usr/lib64/libpython2.7.so -- [3/5] Python Interpreter -- Found PythonInterp: /usr/bin/python (found version "2.7.2") -- [4/5] Numpy Module -- Numpy headers found -- [5/5] SIP Module -- Found sip.h header... -- All python dependencies found - Python support enabled -- GLEW found and GLSL support enabled -- Threaded OpenGL rendering not enabled -- Setting new boost python libraries -- Enabled python terminal -- Python site-packages directory: /usr/lib64/python2.7/site-packages -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -march=amdfam10 -O2 -pipe C++ -march=amdfam10 -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 Linker flags: Executable -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed Module -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed Shared -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build" make -j5 /usr/bin/cmake -H/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3 -B/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory `/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build' make -f libavogadro/src/CMakeFiles/avogadro.dir/build.make libavogadro/src/CMakeFiles/avogadro.dir/depend make[2]: Entering directory `/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles 26 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles 14 /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 1%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 2%] [ 2%] [ 2%] Generating qrc_pythontool.cxx [ 2%] Generating atom.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/rcc -name pythontool -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/qrc_pythontool.cxx /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/pythontool.qrc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/atom.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/atom.h Generating color.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/color.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/color.h Generating fragment.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/fragment.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/fragment.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles Generating mesh.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/mesh.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/mesh.h [ 2%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 2%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles 15 Generating periodictableview.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/periodictableview.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/periodictableview.h Generating moleculefile.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/moleculefile.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/moleculefile.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 3%] Generating periodictablescene_p.moc [ 3%] cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/periodictablescene_p.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/periodictablescene_p.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 3%] Generating cube.moc Generating pluginmanager.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/pluginmanager.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/pluginmanager.h cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/cube.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/cube.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 3%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 3%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles 16 [ 3%] Generating pythontool_p.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/pythontool_p.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/pythontool_p.h Generating residue.moc Generating glwidget.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/glwidget.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/glwidget.h [ 4%] cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/residue.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/residue.h Generating protein.moc /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/protein.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/protein.h [ 4%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles Generating zmatrix.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/zmatrix.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/zmatrix.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 4%] [ 4%] Generating animation.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/animation.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/animation.h Generating plugin.moc /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/plugin.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/plugin.h [ 4%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles Generating toolgroup.moc /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/toolgroup.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/toolgroup.h [ 4%] [ 4%] Generating colorbutton.moc /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles 17 cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/colorbutton.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/colorbutton.h [ 5%] Generating primitive.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/primitive.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/primitive.h Generating pythonengine_p.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/pythonengine_p.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/pythonengine_p.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 5%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles Generating engine.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/engine.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/engine.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 5%] [ 5%] Generating tool.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/tool.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/tool.h Generating molecule.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/molecule.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/molecule.h /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/CMakeFiles [ 5%] Generating elementdetail_p.moc cd /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src && /usr/bin/moc -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -o /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build/libavogadro/src/elementdetail_p.moc /var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3/libavogadro/src/elementdetail_p.h usr/include/boost-1_48/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN" make[2]: *** [libavogadro/src/pythontool_p.moc] Error 1 make[2]: *** Waiting for unfinished jobs.... usr/include/boost-1_48/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN" make[2]: *** [libavogadro/src/pythonengine_p.moc] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build' make[1]: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3_build' make: *** [all] Error 2 emake failed * ERROR: sci-chemistry/avogadro-1.0.3-r1 failed (compile phase): * Make failed! * * Call stack: * ebuild.sh, line 85: Called src_compile * environment, line 5528: Called cmake-utils_src_compile * environment, line 1535: Called _execute_optionaly 'src_compile' * environment, line 566: Called enable_cmake-utils_src_compile * environment, line 1792: Called cmake-utils_src_make * environment, line 1554: Called die * The specific snippet of code: * emake "$@" || die "Make failed!"; * * If you need support, post the output of 'emerge --info =sci-chemistry/avogadro-1.0.3-r1', * the complete build log and the output of 'emerge -pqv =sci-chemistry/avogadro-1.0.3-r1'. * The complete build log is located at '/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/avogadro-1.0.3-r1/work/avogadro-1.0.3'