Bug 683142 – sci-chemistry/openbabel-python-2.4.1-r1::gentoo failed (configure phase) : cmake failed

• Product: Gentoo Linux
• Status: RESOLVED NEEDINFO

[Description Luis Ferreira 2019-04-12 10:29:17 UTC]

emerge -av1 sci-chemistry/openbabel-python

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] sci-chemistry/openbabel-python-2.4.1-r1:0/5::gentoo  PYTHON_TARGETS="python2_7 python3_5 python3_6 (-python3_4%)" 0 KiB

Total: 1 package (1 reinstall), Size of downloads: 0 KiB

Would you like to merge these packages? [Yes/No] y

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) sci-chemistry/openbabel-python-2.4.1-r1::gentoo
 * openbabel-2.4.1.tar.gz BLAKE2B SHA512 size ;-) ...                                                                                                                                                                                                                   [ ok ]
>>> 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_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.


-- Using included inchi library.
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.9") 
-- 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 1.16.0
-- 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               -march=corei7 -O2 -pipe
C++             -march=corei7 -O2 -pipe -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 4023:  Called python_foreach_impl 'my_impl_src_configure'
 *   environment, line 3486:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'my_impl_src_configure'
 *   environment, line 2663:  Called _multibuild_run '_python_multibuild_wrapper' 'my_impl_src_configure'
 *   environment, line 2661:  Called _python_multibuild_wrapper 'my_impl_src_configure'
 *   environment, line  757:  Called my_impl_src_configure
 *   environment, line 4021:  Called cmake-utils_src_configure
 *   environment, line 1136:  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/tmp/sci-chemistry:openbabel-python-2.4.1-r1:20190412-102438.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'

>>> Failed to emerge sci-chemistry/openbabel-python-2.4.1-r1, Log file:

>>>  '/var/tmp/sci-chemistry:openbabel-python-2.4.1-r1:20190412-102438.log'

 * Messages for package sci-chemistry/openbabel-python-2.4.1-r1:
 * Log file: /var/tmp/sci-chemistry:openbabel-python-2.4.1-r1:20190412-102438.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 4023:  Called python_foreach_impl 'my_impl_src_configure'
 *   environment, line 3486:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'my_impl_src_configure'
 *   environment, line 2663:  Called _multibuild_run '_python_multibuild_wrapper' 'my_impl_src_configure'
 *   environment, line 2661:  Called _python_multibuild_wrapper 'my_impl_src_configure'
 *   environment, line  757:  Called my_impl_src_configure
 *   environment, line 4021:  Called cmake-utils_src_configure
 *   environment, line 1136:  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/tmp/sci-chemistry:openbabel-python-2.4.1-r1:20190412-102438.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'

[Comment 1 Jonas Stein 2019-04-16 21:17:58 UTC]

Thank you for the report. Please recompile and 
*attach* the logfiles and 
paste the emerge info as described on
https://wiki.gentoo.org/wiki/Attach_the_logs_to_the_bug_ticket
The logs must be part of the ticket, but not on external websites.
We need to have all information at hand before ticket assignment, so that the maintainer can look after it in one session with minimal number of callbacks.
Please reopen this ticket (Status:unconfirmed) afterwards.

[Comment 2 Luis Ferreira 2019-04-17 08:31:20 UTC]

Created attachment 573144 [details]
emerge --info '=sci-chemistry/openbabel-python-2.4.1-r1::gentoo'

[Comment 3 Luis Ferreira 2019-04-17 08:32:58 UTC]

Created attachment 573146 [details]
sci-chemistry/openbabel-python-2.4.1-r1/temp/build.log

[Comment 4 Luis Ferreira 2019-04-17 08:41:00 UTC]

Created attachment 573148 [details]
emerge -pqv '=sci-chemistry/openbabel-python-2.4.1-r1::gentoo'