* Package: sci-chemistry/avogadro-1.1.1  * Repository: gentoo  * Maintainer: sci-chemistry@gentoo.org  * USE: abi_x86_64 amd64 cpu_flags_x86_sse2 elibc_glibc glsl kernel_linux python_targets_python2_7 userland_GNU  * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking avogadro-1.1.1.tar.bz2 to /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 ... * Applying avogadro-1.1.0-xlibs.patch ...  [ ok ] * Applying avogadro-1.1.1-eigen3.patch ...  [ ok ] * Applying avogadro-1.1.1-mkspecs-dir.patch ...  [ ok ] * Applying avogadro-1.1.1-no-strip.patch ...  [ ok ] * Applying avogadro-1.1.1-pkgconfig_eigen.patch ...  [ ok ] * Applying avogadro-1.1.1-openbabel.patch ...  [ ok ] * Applying avogadro-1.1.1-boost-join-moc.patch ...  [ ok ] * Applying patches from /etc/portage/patches/sci-chemistry/avogadro-1.1.1 ... * proposed.patch ...  [ ok ] * User patches applied. >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build" cmake -C /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DENABLE_THREADEDGL=OFF -DENABLE_RPATH=OFF -DENABLE_UPDATE_CHECKER=OFF -DQT_MKSPECS_DIR=/usr/share/qt4/mkspecs -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs -DENABLE_glsl=yes -DENABLE_TESTS=no -DWITH_SSE2=yes -DENABLE_python=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 loading initial cache file /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/gentoo_common_config.cmake -- The C compiler identification is GNU 6.3.0 -- The CXX compiler identification is GNU 6.3.0 -- 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 -- The build type is Gentoo -- Performing Test HAVE_NO_RTTI -- Performing Test HAVE_NO_RTTI - Success -- Performing Test HAVE_RTTI -- Performing Test HAVE_RTTI - Success -- 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/lib64/qt4/bin/qmake (found suitable version "4.8.7", minimum required is "4.6.0") -- Found OpenGL: /usr/lib/libGL.so -- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/libXext.so -- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/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/lib/libX11.so -- Found lupdate: /usr/bin/lupdate -- Found lrelease: /usr/bin/lrelease -- Found lconvert: /usr/bin/lconvert -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "0.29.2") -- Checking for module 'openbabel-2.0>=2.3.0' -- Found openbabel-2.0, version 2.4.1 -- Found OpenBabel 2.3 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: 1.63.0 -- Found the following Boost libraries: -- python -- Boost Python found... -- [2/5] Python Libraries -- Found PythonLibs: /usr/lib/libpython2.7.so -- [3/5] Python Interpreter -- Found PythonInterp: /usr/bin/python (found version "3.4.6") -- [4/5] Numpy Module File "", line 1 import numpy; print numpy.get_include() ^ SyntaxError: invalid syntax -- Numpy NOT found - Python support disabled. CMake Warning at CMakeLists.txt:280 (message): Not all python dependencies are found - Python support diabled -- Threaded OpenGL rendering not enabled -- Found Qt4: /usr/lib64/qt4/bin/qmake (found suitable version "4.8.7", minimum required is "4.6") -- Linking in static plugins: bsdyengine;navigatetool;elementcolor -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- docbook tools not found, doc targets disabled -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe C++ -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 CMake Warning (dev) in libavogadro/src/CMakeLists.txt: Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link interface. Run "cmake --help-policy CMP0022" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Target "avogadro" has an INTERFACE_LINK_LIBRARIES property which differs from its LINK_INTERFACE_LIBRARIES properties. INTERFACE_LINK_LIBRARIES: openbabel;/usr/lib64/qt4/libQtOpenGL.so;/usr/lib64/qt4/libQtGui.so;/usr/lib64/qt4/libQtCore.so;/usr/lib/libGLU.so;/usr/lib/libGL.so;bsdyengine;navigatetool;elementcolor LINK_INTERFACE_LIBRARIES: This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt: Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link interface. Run "cmake --help-policy CMP0022" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Target "OpenQube" has an INTERFACE_LINK_LIBRARIES property which differs from its LINK_INTERFACE_LIBRARIES properties. INTERFACE_LINK_LIBRARIES: $<$>:/usr/lib64/qt4/libQtCore.so>;$<$:/usr/lib64/qt4/libQtCore.so> LINK_INTERFACE_LIBRARIES: This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done CMake Warning: Manually-specified variables were not used by the project: ENABLE_glsl ENABLE_python QT_MKSPECS_RELATIVE -- Build files have been written to: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build" make -j4 VERBOSE=1 /usr/bin/cmake -H/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 -B/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/CMakeFiles /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make -f libavogadro/src/colors/CMakeFiles/elementcolor.dir/build.make libavogadro/src/colors/CMakeFiles/elementcolor.dir/depend make -f libavogadro/src/engines/CMakeFiles/bsdyengine.dir/build.make libavogadro/src/engines/CMakeFiles/bsdyengine.dir/depend make -f libavogadro/src/tools/CMakeFiles/navigatetool.dir/build.make libavogadro/src/tools/CMakeFiles/navigatetool.dir/depend make -f libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/build.make libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography/spglib /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/DependInfo.cmake --color= [ 1%] Generating moc_elementcolor.cxx cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/colors && /usr/lib64/qt4/bin/moc @/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/colors/moc_elementcolor.cxx_parameters [ 1%] Generating ui_bsdysettingswidget.h [ 1%] Generating qrc_navigatetool.cxx cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines && /usr/lib64/qt4/bin/uic -o /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/ui_bsdysettingswidget.h /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/engines/bsdysettingswidget.ui cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools && /usr/lib64/qt4/bin/rcc -name navigatetool -o /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools/qrc_navigatetool.cxx /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.qrc Dependee "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/depend.internal". Scanning dependencies of target spglib make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make -f libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/build.make libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' [ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/cell.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-linux-gnu-gcc -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fPIC -w -o CMakeFiles/spglib.dir/cell.c.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography/spglib/cell.c [ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/debug.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-linux-gnu-gcc -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fPIC -w -o CMakeFiles/spglib.dir/debug.c.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography/spglib/debug.c [ 1%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/hall_symbol.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-linux-gnu-gcc -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fPIC -w -o CMakeFiles/spglib.dir/hall_symbol.c.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography/spglib/hall_symbol.c [ 1%] Generating moc_bsdyengine.cxx cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines && /usr/lib64/qt4/bin/moc 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Scanning dependencies of target navigatetool [ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-linux-gnu-gcc -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fPIC -w -o CMakeFiles/spglib.dir/symmetry.c.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography/spglib/symmetry.c [ 2%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/symmetry_kpoint.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-linux-gnu-gcc -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/crystallography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/crystallography -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fPIC -w -o CMakeFiles/spglib.dir/symmetry_kpoint.c.o -c 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CMakeFiles/spglib.dir/spglib.c.o CMakeFiles/spglib.dir/symmetry.c.o CMakeFiles/spglib.dir/symmetry_kpoint.c.o /usr/bin/x86_64-pc-linux-gnu-ranlib libspglib.a make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' [ 3%] Built target spglib make -f libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/build.make libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' [ 3%] Generating moc_slaterset.cxx cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube && /usr/lib64/qt4/bin/moc @/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/moc_slaterset.cxx_parameters cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/engines /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/CMakeFiles/bsdyengine.dir/DependInfo.cmake --color= Dependee "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/CMakeFiles/bsdyengine.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/CMakeFiles/bsdyengine.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/CMakeFiles/bsdyengine.dir/depend.internal". Scanning dependencies of target bsdyengine [ 3%] Generating moc_basisset.cxx cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube && /usr/lib64/qt4/bin/moc @/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/moc_basisset.cxx_parameters [ 3%] Generating moc_gaussianset.cxx cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube && /usr/lib64/qt4/bin/moc @/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/moc_gaussianset.cxx_parameters cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1 /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/DependInfo.cmake --color= Dependee "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/depend.internal". Scanning dependencies of target OpenQube make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make -f libavogadro/src/colors/CMakeFiles/elementcolor.dir/build.make libavogadro/src/colors/CMakeFiles/elementcolor.dir/build make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make -f libavogadro/src/engines/CMakeFiles/bsdyengine.dir/build.make libavogadro/src/engines/CMakeFiles/bsdyengine.dir/build make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make -f libavogadro/src/tools/CMakeFiles/navigatetool.dir/build.make libavogadro/src/tools/CMakeFiles/navigatetool.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' [ 3%] Building CXX object libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/colors && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/colors -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -DQT_STATICPLUGIN -fPIC -o CMakeFiles/elementcolor.dir/elementcolor.cpp.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/colors/elementcolor.cpp [ 3%] Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -DQT_STATICPLUGIN -fPIC -o CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.cpp [ 3%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -DQT_STATICPLUGIN -fPIC -o CMakeFiles/navigatetool.dir/navigatetool.cpp.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/glwidget.h:32:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.h:29, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:26: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/primitive.h:34:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/colors/elementcolor.cpp:27: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/primitive.h:34:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/primitivelist.h:29, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/engine.h:37, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.h:29, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.cpp:25: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make -f libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/build.make libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' [ 3%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/atom.cpp.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces/openqube && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DOpenQube_EXPORTS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/extensions/surfaces -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -fPIC -o CMakeFiles/OpenQube.dir/atom.cpp.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/atom.cpp In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/molecule.h:25:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/atom.h:20, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/atom.cpp:17: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ make[2]: *** [libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/build.make:78: libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/atom.cpp.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[1]: *** [CMakeFiles/Makefile2:2359: libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... [ 3%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -DQT_STATICPLUGIN -fPIC -o CMakeFiles/navigatetool.dir/eyecandy.cpp.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/eyecandy.cpp In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/eyecandy.h:28:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/eyecandy.cpp:26: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/navigate.h:30:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:31: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:103:38: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type void setModelview(const Eigen::Transform3d &matrix); ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:107:20: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type const Eigen::Transform3d & modelview() const; ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:111:14: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type Eigen::Transform3d & modelview(); ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h: In member function ‘Eigen::Vector3d Avogadro::Camera::V4toV3DivW(const Vector4d&)’: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:343:19: error: ‘const Vector4d {aka const class Eigen::Matrix}’ has no member named ‘start’; did you mean ‘sqrt’? return v4.start<3>()/v4.w(); ^~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:343:28: error: expected primary-expression before ‘)’ token return v4.start<3>()/v4.w(); ^ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp: In member function ‘void Avogadro::NavigateTool::computeReferencePoint(Avogadro::GLWidget*)’: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/navigatetool.cpp:95:57: error: ‘class Avogadro::Camera’ has no member named ‘modelview’; did you mean ‘setModelview’? Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos(); ^~~~~~~~~ make[2]: *** [libavogadro/src/colors/CMakeFiles/elementcolor.dir/build.make:68: libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[1]: *** [CMakeFiles/Makefile2:2726: libavogadro/src/colors/CMakeFiles/elementcolor.dir/all] Error 2 [ 3%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/moc_navigatetool.cxx.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -DQT_STATICPLUGIN -fPIC -o CMakeFiles/navigatetool.dir/moc_navigatetool.cxx.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools/moc_navigatetool.cxx make[2]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/build.make:78: libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs.... [ 3%] Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/moc_bsdyengine.cxx.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines && /usr/bin/x86_64-pc-linux-gnu-g++ -DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_DEFAULT_SOURCE -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -I/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING -DNDEBUG -O2 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -DQT_STATICPLUGIN -fPIC -o CMakeFiles/bsdyengine.dir/moc_bsdyengine.cxx.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/moc_bsdyengine.cxx In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/engines/bsdyengine.cpp:27:0: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:103:38: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type void setModelview(const Eigen::Transform3d &matrix); ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:107:20: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type const Eigen::Transform3d & modelview() const; ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:111:14: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type Eigen::Transform3d & modelview(); ^~~~~~~~~~~ In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/glwidget.h:32:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools/../../../../avogadro-1.1.1/libavogadro/src/tools/navigatetool.h:29, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/tools/moc_navigatetool.cxx:9: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h: In member function ‘Eigen::Vector3d Avogadro::Camera::V4toV3DivW(const Vector4d&)’: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:343:19: error: ‘const Vector4d {aka const class Eigen::Matrix}’ has no member named ‘start’; did you mean ‘sqrt’? return v4.start<3>()/v4.w(); ^~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:343:28: error: expected primary-expression before ‘)’ token return v4.start<3>()/v4.w(); ^ In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/primitive.h:34:0, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/primitivelist.h:29, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/engine.h:37, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/../../../../avogadro-1.1.1/libavogadro/src/engines/bsdyengine.h:29, from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/src/engines/moc_bsdyengine.cxx:9: /usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information ^~~~~ In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/tools/eyecandy.cpp:29:0: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:103:38: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type void setModelview(const Eigen::Transform3d &matrix); ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:107:20: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type const Eigen::Transform3d & modelview() const; ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:111:14: error: ‘Transform3d’ in namespace ‘Eigen’ does not name a type Eigen::Transform3d & modelview(); ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h: In member function ‘Eigen::Vector3d Avogadro::Camera::V4toV3DivW(const Vector4d&)’: /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:343:19: error: ‘const Vector4d {aka const class Eigen::Matrix}’ has no member named ‘start’; did you mean ‘sqrt’? return v4.start<3>()/v4.w(); ^~~~~ /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/camera.h:343:28: error: expected primary-expression before ‘)’ token return v4.start<3>()/v4.w(); ^ make[2]: *** [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/build.make:72: libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/build.make:102: libavogadro/src/tools/CMakeFiles/navigatetool.dir/eyecandy.cpp.o] Error 1 make[2]: *** [libavogadro/src/tools/CMakeFiles/navigatetool.dir/build.make:126: libavogadro/src/tools/CMakeFiles/navigatetool.dir/moc_navigatetool.cxx.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[1]: *** [CMakeFiles/Makefile2:1208: libavogadro/src/tools/CMakeFiles/navigatetool.dir/all] Error 2 make[2]: *** [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/build.make:96: libavogadro/src/engines/CMakeFiles/bsdyengine.dir/moc_bsdyengine.cxx.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make[1]: *** [CMakeFiles/Makefile2:800: libavogadro/src/engines/CMakeFiles/bsdyengine.dir/all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' make: *** [Makefile:152: all] Error 2 * ERROR: sci-chemistry/avogadro-1.1.1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/avogadro-1.1.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/avogadro-1.1.1::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build' * S: '/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1'