sci-libs:cctbx-2010.03.29.2334-r7:20170907-140319.log

sci-libs:cctbx-2010.03.29.2334-r7:20170907-140319.log (text/plain), 14.83 KB, created by Toralf Förster on 2017-09-07 15:22:08 UTC

 * Package:    sci-libs/cctbx-2010.03.29.2334-r7
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux minimal openmp python_targets_python2_7 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
 * Using following Fortran compiler:
 *   F77: x86_64-pc-linux-gnu-gfortran
 *   FC:  x86_64-pc-linux-gnu-gfortran
 * x86_64-pc-linux-gnu-gfortran has OPENMP support
>>> Unpacking source...
>>> Unpacking cctbx-2010.03.29.2334.tar.gz to /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work
>>> Source unpacked in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work
>>> Preparing source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work ...
 * Applying 2010.03.29.2334-tst_server.py.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-boost.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-clipper.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-flags.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-soname.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-gcc-4.6.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-gcc-4.7.patch ...
 [ ok ]
 * Applying 2010.03.29.2334-format-security.patch ...
 [ ok ]
 * Adjusting to prefix /
 *   libtbx_refresh.py ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work ...
 * configuring with  /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/libtbx/configure.py --compiler=gcc --enable-openmp-if-possible=true  --scan-boost --use_environment_flags --current_working_directory=/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable
Python: 2.7.13 "/usr/bin/python2.7"
Compiler: gcc
Build mode: release
Warning level: 0
Static libraries: False
Static exe: False
Scan Boost headers: True
Write full flex_fwd.h files: False
Build Boost.Python extensions: True
Define BOOST_PYTHON_NO_PY_SIGNATURES: False
Define BOOST_PYTHON_BOOL_INT_STRICT: True
Boost threads enabled: False
Enable OpenMP if possible: True
Use environment flags: True
  CXXFLAGS =  -Werror=terminate -O2 -pipe -march=native
  CFLAGS =  -O2 -pipe -march=native -Wall
  CPPFLAGS =  
  LDFLAGS =  -Wl,-O1 -Wl,--as-needed
command_version_suffix: None
Top-down list of all modules involved:
  fftw3tbx         /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/fftw3tbx
  rstbx            /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx
  smtbx            /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/smtbx
  mmtbx            /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx
  iotbx            /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx
  ccp4io+adaptbx   /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io
                   /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io_adaptbx
  clipper+adaptbx  /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/clipper
                   /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/clipper_adaptbx
  cctbx            /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx
  scitbx           /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx
  omptbx           /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/omptbx
  chiltbx          /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/chiltbx
  fable            /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/fable
  boost_adaptbx    /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx
  libtbx           /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/libtbx
Creating files in build directory:
  "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build"
    dispatcher_include_template.sh
    dispatcher_head.sh
    setpaths.sh
    setpaths.csh
    setpaths_all.sh
    setpaths_all.csh
    setpaths_debug.sh
    unsetpaths.sh
    setpaths_debug.csh
    unsetpaths.csh
    SConstruct
    Makefile
    run_tests.csh
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/libtbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/fable/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/smtbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/fftw3tbx/command_line"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/libtbx/libtbx_refresh.py"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/libtbx_refresh.py"
  Generating C++ header files in:
    "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build/include/scitbx/array_family"
********************************************************
Warning: unexpected md5 hexdigest:
  File: "/usr/include/boost/random/mersenne_twister.hpp"
  New md5 hexdigest: b85f4dfb855d9cb6dd8d17d89b61dc52
  Files to review:
    scitbx/random.h
    scitbx/libtbx_refresh.py
********************************************************
  Generating C++ files in:
    "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build/include/scitbx/array_family/boost_python"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/libtbx_refresh.py"
  Generating C++ files in:
    "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build/cctbx/eltbx"
  Generating C++ files in:
    "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build/include/cctbx/boost_python"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/smtbx/libtbx_refresh.py"
  Generating C++ files in:
    "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build/include/smtbx/boost_python"
Processing: "/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/fftw3tbx/libtbx_refresh.py"
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work ...
 * compiling with libtbx.scons -j 1
scons: Reading SConscript files ...
libtbx.scons: using flags from initial environment: 
              CXXFLAGS =  -Werror=terminate -O2 -pipe -march=native
              CFLAGS =  -O2 -pipe -march=native -Wall
              CPPFLAGS =  
libtbx.scons: OpenMP is available.
scons: done reading SConscript files.
scons: Building targets ...
g++ -o boost_adaptbx/hybrid_times_ext.o -c -Werror=terminate -O2 -pipe -march=native -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -O2 -pipe -march=native -Wall -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/hybrid_times_ext.cpp
g++ -o boost_adaptbx/meta_ext.o -c -Werror=terminate -O2 -pipe -march=native -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -O2 -pipe -march=native -Wall -fopenmp -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/meta_ext.cpp
g++ -o boost_adaptbx/optional_ext.o -c -Werror=terminate -O2 -pipe -march=native -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -O2 -pipe -march=native -Wall -fopenmp -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/optional_ext.cpp
g++ -o boost_adaptbx/rational_ext.o -c -Werror=terminate -O2 -pipe -march=native -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -O2 -pipe -march=native -Wall -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/rational_ext.cpp
In file included from /usr/include/boost/preprocessor/iteration/detail/iter/forward1.hpp:47:0,
                 from /usr/include/boost/python/detail/invoke.hpp:61,
                 from /usr/include/boost/python/detail/caller.hpp:16,
                 from /usr/include/boost/python/object/function_handle.hpp:8,
                 from /usr/include/boost/python/converter/arg_to_python.hpp:19,
                 from /usr/include/boost/python/call.hpp:15,
                 from /usr/include/boost/python/object_core.hpp:14,
                 from /usr/include/boost/python/args.hpp:22,
                 from /usr/include/boost/python/make_function.hpp:11,
                 from /usr/include/boost/python/def.hpp:11,
                 from /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/rational_ext.cpp:2:
/usr/include/boost/python/detail/invoke.hpp: In instantiation of 'PyObject* boost::python::detail::invoke(boost::python::detail::invoke_tag_<false, true>, const RC&, F&, TC&) [with RC = boost::python::detail::specify_a_return_value_policy_to_wrap_functions_returning<const int&>; F = const int& (boost::rational<int>::*)() const; TC = boost::python::arg_from_python<boost::rational<int>&>; PyObject = _object]':
/usr/include/boost/python/detail/caller.hpp:216:46:   required from 'PyObject* boost::python::detail::caller_arity<1u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = const int& (boost::rational<int>::*)() const; Policies = boost::python::default_call_policies; Sig = boost::mpl::vector2<const int&, boost::rational<int>&>; PyObject = _object]'
/usr/include/boost/python/object/py_function.hpp:38:33:   required from 'PyObject* boost::python::objects::caller_py_function_impl<Caller>::operator()(PyObject*, PyObject*) [with Caller = boost::python::detail::caller<const int& (boost::rational<int>::*)() const, boost::python::default_call_policies, boost::mpl::vector2<const int&, boost::rational<int>&> >; PyObject = _object]'
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/rational_ext.cpp:158:1:   required from here
/usr/include/boost/python/detail/invoke.hpp:86:14: error: no match for call to '(const boost::python::detail::specify_a_return_value_policy_to_wrap_functions_returning<const int&>) (const int&)'
     return rc( (tc().*f)(BOOST_PP_ENUM_BINARY_PARAMS_Z(1, N, ac, () BOOST_PP_INTERCEPT)) );
            ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/python/object/function_handle.hpp:8:0,
                 from /usr/include/boost/python/converter/arg_to_python.hpp:19,
                 from /usr/include/boost/python/call.hpp:15,
                 from /usr/include/boost/python/object_core.hpp:14,
                 from /usr/include/boost/python/args.hpp:22,
                 from /usr/include/boost/python/make_function.hpp:11,
                 from /usr/include/boost/python/def.hpp:11,
                 from /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/rational_ext.cpp:2:
/usr/include/boost/python/detail/caller.hpp: In instantiation of 'static const PyTypeObject* boost::python::detail::converter_target_type<ResultConverter>::get_pytype() [with ResultConverter = boost::python::detail::specify_a_return_value_policy_to_wrap_functions_returning<const int&>; PyTypeObject = _typeobject]':
/usr/include/boost/python/detail/caller.hpp:238:19:   required from 'static boost::python::detail::py_func_sig_info boost::python::detail::caller_arity<1u>::impl<F, Policies, Sig>::signature() [with F = const int& (boost::rational<int>::*)() const; Policies = boost::python::default_call_policies; Sig = boost::mpl::vector2<const int&, boost::rational<int>&>]'
/usr/include/boost/python/object/py_function.hpp:48:35:   required from 'boost::python::detail::py_func_sig_info boost::python::objects::caller_py_function_impl<Caller>::signature() const [with Caller = boost::python::detail::caller<const int& (boost::rational<int>::*)() const, boost::python::default_call_policies, boost::mpl::vector2<const int&, boost::rational<int>&> >]'
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/rational_ext.cpp:158:1:   required from here
/usr/include/boost/python/detail/caller.hpp:100:98: error: 'struct boost::python::detail::specify_a_return_value_policy_to_wrap_functions_returning<const int&>' has no member named 'get_pytype'
 converter((PyObject*)0, (ResultConverter *)0, (ResultConverter *)0).get_pytype();
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
scons: *** [boost_adaptbx/rational_ext.o] Error 1
scons: building terminated because of errors.
 * ERROR: sci-libs/cctbx-2010.03.29.2334-r7::gentoo failed (compile phase):
 *   make failed
 * 
 * Call stack:
 *     ebuild.sh, line 115:  Called src_compile
 *   environment, line 3188:  Called die
 * The specific snippet of code:
 *       libtbx.scons ${makeopts_exp} . || die "make failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/cctbx-2010.03.29.2334-r7::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/cctbx-2010.03.29.2334-r7::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-libs:cctbx-2010.03.29.2334-r7:20170907-140319.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_build'
 * S: '/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work'