sci-chemistry:openbabel-python-2.4.1-r1:20180824-175001.log

sci-chemistry:openbabel-python-2.4.1-r1:20180824-175001.log (text/plain), 10.12 KB, created by Toralf Förster on 2018-08-24 17:54:01 UTC

 * Package:    sci-chemistry/openbabel-python-2.4.1-r1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_6 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking openbabel-2.4.1.tar.gz to /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1 ...
 * Applying openbabel-python-2.3.2-gcc-6_and_7-backport.patch ...
 [ ok ]
/usr/include/openbabel-2.0/openbabel/obconversion.h:369: Warning 325: Nested struct not currently supported (StreamState ignored)
/usr/include/openbabel-2.0/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored)
/usr/include/openbabel-2.0/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored).
/usr/include/openbabel-2.0/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored).
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1 ...
 * python2_7: running my_impl_src_configure
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7"
cmake -C /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH= -DBINDINGS_ONLY=ON -DBABEL_SYSTEM_LIBRARY=/usr/lib64/libopenbabel.so -DOB_MODULE_PATH=/usr/lib64/openbabel/2.4.1 -DLIB_INSTALL_DIR=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/image//usr/lib64/python2.7/site-packages -DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python2.7 -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_INCLUDE_PATH=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib64/libpython2.7.so -DENABLE_TESTS=ON -DCMAKE_INSTALL_PREFIX=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/image/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1
loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/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
CMake Deprecation Warning at CMakeLists.txt:16 (cmake_policy):
  The OLD behavior for policy CMP0005 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


CMake Deprecation Warning at CMakeLists.txt:18 (cmake_policy):
  The OLD behavior for policy CMP0042 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


-- Using included inchi library.
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.8") 
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") 
-- Found wxWidgets: -L/usr/lib64;-pthread;;;-lwx_baseu-3.0;-lwx_gtk2u_core-3.0;-lwx_gtk2u_adv-3.0 (found version "3.0.4") 
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - not found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH):
  MATH cannot parse the expression: "x86_648*10000 + x86_642*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:248 (macro_ensure_version)


CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH):
  MATH cannot parse the expression: "x86_648*10000 + x86_642*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:249 (macro_ensure_version)


CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH):
  MATH cannot parse the expression: "x86_648*10000 + x86_642*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:250 (macro_ensure_version)


-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success
-- Use std::shared_ptr in memory
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "0.29.2") 
-- Checking for module 'cairo'
--   Found cairo, version 1.14.12
-- Found Cairo: /usr/lib/libcairo.so  
-- Cairo found. PNG output will be supported.
-- Looking for getopt
-- Looking for getopt - found
-- Attempting to build the GUI
--    wxWidgets found => GUI will be built
-- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.15") 
-- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.15") 
-- Python bindings will be compiled
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/image/usr
Compiler flags:
C               -O2 -pipe -march=native
C++             -O2 -pipe -march=native -pthread
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/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/CMakeFiles/CMakeOutput.log".
See also "/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7/CMakeFiles/CMakeError.log".
 * ERROR: sci-chemistry/openbabel-python-2.4.1-r1::gentoo failed (configure phase):
 *   cmake failed
 * 
 * Call stack:
 *     ebuild.sh, line  124:  Called src_configure
 *   environment, line 3964:  Called python_foreach_impl 'my_impl_src_configure'
 *   environment, line 3428:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'my_impl_src_configure'
 *   environment, line 2606:  Called _multibuild_run '_python_multibuild_wrapper' 'my_impl_src_configure'
 *   environment, line 2604:  Called _python_multibuild_wrapper 'my_impl_src_configure'
 *   environment, line  706:  Called my_impl_src_configure
 *   environment, line 3962:  Called cmake-utils_src_configure
 *   environment, line 1079:  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/openbabel-python-2.4.1-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-python-2.4.1-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:openbabel-python-2.4.1-r1:20180824-175001.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1-python2_7'
 * S: '/var/tmp/portage/sci-chemistry/openbabel-python-2.4.1-r1/work/openbabel-2.4.1'