* Package: sci-libs/cctbx-2010.03.29.2334-r7 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * 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_, const RC&, F&, TC&) [with RC = boost::python::detail::specify_a_return_value_policy_to_wrap_functions_returning; F = const int& (boost::rational::*)() const; TC = boost::python::arg_from_python&>; PyObject = _object]': /usr/include/boost/python/detail/caller.hpp:216:46: required from 'PyObject* boost::python::detail::caller_arity<1u>::impl::operator()(PyObject*, PyObject*) [with F = const int& (boost::rational::*)() const; Policies = boost::python::default_call_policies; Sig = boost::mpl::vector2&>; PyObject = _object]' /usr/include/boost/python/object/py_function.hpp:38:33: required from 'PyObject* boost::python::objects::caller_py_function_impl::operator()(PyObject*, PyObject*) [with Caller = boost::python::detail::caller::*)() const, boost::python::default_call_policies, boost::mpl::vector2&> >; 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&)' 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::get_pytype() [with ResultConverter = boost::python::detail::specify_a_return_value_policy_to_wrap_functions_returning; 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::signature() [with F = const int& (boost::rational::*)() const; Policies = boost::python::default_call_policies; Sig = boost::mpl::vector2&>]' /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::signature() const [with Caller = boost::python::detail::caller::*)() const, boost::python::default_call_policies, boost::mpl::vector2&> >]' /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' 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'