sci-chemistry:openbabel-2.4.1-r1:20200516-194354.log

sci-chemistry:openbabel-2.4.1-r1:20200516-194354.log (text/plain), 9.21 KB, created by Toralf Förster on 2020-05-16 19:49:46 UTC

 * Package:    sci-chemistry/openbabel-2.4.1-r1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux openmp 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-2.4.1-r1/work
>>> Unpacking openbabel.png to /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work
unpack openbabel.png: file format not recognized. Ignoring.
>>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1 ...
 * Applying openbabel-2.3.2-gcc-6_and_7-backport.patch ...
 [ ok ]
 * Applying openbabel-2.4.1-gcc-8.patch ...
 [ ok ]
 * Hardcoded definition(s) removed in CMakeLists.txt:
 *     set(CMAKE_BUILD_TYPE RelWithDebInfo)
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build"
cmake -C /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DOPENBABEL_USE_SYSTEM_INCHI=ON -DENABLE_OPENMP=yes -DBUILD_GUI=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1
loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 10.1.0
-- The CXX compiler identification is GNU 10.1.0
-- 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.


CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:272 (message):
  The package name passed to `find_package_handle_standard_args` (INCHI) does
  not match the name of the calling package (Inchi).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/modules/FindInchi.cmake:19 (find_package_handle_standard_args)
  CMakeLists.txt:149 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found INCHI: /usr/lib64/libinchi.so  
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.9") 
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES wxWidgets_INCLUDE_DIRS) 
-- 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_6410*10000 + x86_641*100 + x86_640":
  syntax error, unexpected exp_NUMBER, expecting $end (9).
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_6410*10000 + x86_641*100 + x86_640":
  syntax error, unexpected exp_NUMBER, expecting $end (9).
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_6410*10000 + x86_641*100 + x86_640":
  syntax error, unexpected exp_NUMBER, expecting $end (9).
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 OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "1.6.3") 
-- Checking for module 'cairo'
--   Found cairo, version 1.16.0
-- Found Cairo: /usr/lib64/libcairo.so  
-- Cairo found. PNG output will be supported.
-- Looking for getopt
-- Looking for getopt - found
-- GUI will not be built
-- Found PythonInterp: /usr/bin/python (found version "3.8.3") 
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -pipe -march=native -fopenmp
C++             -O2 -pipe -march=native -fopenmp
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 -Wl,--defsym=__gentoo_check_ldflags__=0 
Module          -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring incomplete, errors occurred!
See also "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/CMakeFiles/CMakeOutput.log".
See also "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/CMakeFiles/CMakeError.log".
 * ERROR: sci-chemistry/openbabel-2.4.1-r1::gentoo failed (configure phase):
 *   cmake failed
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_configure
 *   environment, line 2494:  Called cmake-utils_src_configure
 *   environment, line  973:  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-2.4.1-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-2.4.1-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:openbabel-2.4.1-r1:20200516-194354.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build'
 * S: '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1'