Since I changed to a new 17.0 profile, avogadro-1.1.1 fails to build, maybe due to gcc-6.4.0 and not the profile itself: ===== * 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 ] >>> 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 6.4.0 -- The CXX compiler identification is GNU 6.4.0 -- 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 CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH): math cannot parse the expression: "x86_646*10000 + x86_644*100 + x86_640": syntax error, unexpected exp_NUMBER, expecting $end (8) Call Stack (most recent call first): cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION) CMakeLists.txt:98 (macro_ensure_version) CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH): math cannot parse the expression: "x86_646*10000 + x86_644*100 + x86_640": syntax error, unexpected exp_NUMBER, expecting $end (8) Call Stack (most recent call first): cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION) CMakeLists.txt:99 (macro_ensure_version) -- 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 "2.7.14") -- [4/5] Numpy Module -- Numpy headers found -- [5/5] SIP Module -- SIP version 267009 found -- Found SIP: /usr/include/python2.7 -- All python dependencies found - Python support enabled -- Threaded OpenGL rendering not enabled -- Setting new boost python libraries -- Enabled python terminal -- 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 -- Python site-packages directory: /usr/lib64/python2.7/site-packages -- 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 -march=native -O2 -pipe C++ -march=native -O2 -pipe -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 incomplete, errors occurred! See also "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/CMakeFiles/CMakeOutput.log". See also "/var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/CMakeFiles/CMakeError.log". * ERROR: sci-chemistry/avogadro-1.1.1::gentoo failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 124: Called src_configure * environment, line 4072: Called cmake-utils_src_configure * environment, line 1096: Called die * The specific snippet of code: * "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake 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' === Since there's an old open bug for v.1.2.0 (https://bugs.gentoo.org/594630), perhaps the updated version could compile with the newer gcc.
Same error for versions 1.0.3-r2 and 1.1.0. No version in the tree compiles on my system.
Duplicate of bug #619544
*** This bug has been marked as a duplicate of bug 619544 ***
