* Package: sci-libs/cctbx-2010.03.29.2334-r7 * Repository: gentoo * Maintainer: jlec@gentoo.org sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux minimal openmp python_targets_python2_7 userland_GNU * FEATURES: 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 * 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 ] * Adjusting to prefix / * libtbx_refresh.py ... [ ok ] * 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: 2.7.9 "/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 = -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 CFLAGS = -march=native -Wformat -Werror=format-security -g0 -O2 CPPFLAGS = LDFLAGS = -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu 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: 043fb8e15149e2fe8c5b59cd5ff465a7 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" * compiling with libtbx.scons -j 8 [?1034hscons: Reading SConscript files ... libtbx.scons: using flags from initial environment: CXXFLAGS = -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 CFLAGS = -march=native -Wformat -Werror=format-security -g0 -O2 CPPFLAGS = libtbx.scons: OpenMP is available. scons: done reading SConscript files. scons: Building targets ... g++ -o boost_adaptbx/hybrid_times_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 g++ -o boost_adaptbx/std_pair_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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/std_pair_ext.cpp g++ -o boost_adaptbx/tests/python_streambuf_test_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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/tests/python_streambuf_test_ext.cpp g++ -o boost_adaptbx/tests/tst_optional_copy.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/boost_adaptbx/tests/tst_optional_copy.cpp g++ -o boost_adaptbx/tuple_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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/tuple_ext.cpp g++ -o boost_adaptbx/tests/tst_optional_copy -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp boost_adaptbx/tests/tst_optional_copy.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib gcc -o ccp4io/lib/src/ccp4_array.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/ccp4_array.c gcc -o ccp4io/lib/src/ccp4_parser.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/ccp4_parser.c gcc -o ccp4io/lib/src/ccp4_unitcell.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/ccp4_unitcell.c gcc -o ccp4io/lib/src/cmap_accessor.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_accessor.c gcc -o ccp4io/lib/src/cmap_close.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_close.c gcc -o ccp4io/lib/src/cmap_data.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_data.c gcc -o ccp4io/lib/src/cmap_header.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_header.c gcc -o ccp4io/lib/src/cmap_labels.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_labels.c gcc -o ccp4io/lib/src/cmap_open.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_open.c gcc -o ccp4io/lib/src/cmap_skew.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_skew.c gcc -o ccp4io/lib/src/cmap_stats.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_stats.c gcc -o ccp4io/lib/src/cmap_symop.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmap_symop.c gcc -o ccp4io/lib/src/cmtzlib.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cmtzlib.c gcc -o ccp4io/lib/src/cvecmat.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/cvecmat.c gcc -o ccp4io/lib/src/library_err.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/library_err.c gcc -o ccp4io/lib/src/library_file.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/library_file.c gcc -o ccp4io/lib/src/library_utils.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src/library_utils.c gcc -o ccp4io_adaptbx/csymlib.o -c -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I. -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src ccp4io_adaptbx/csymlib.c g++ -o cctbx/adp_restraints/adp_restraints_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adp_restraints/adp_similarity.cpp g++ -o cctbx/adp_restraints/adp_similarity_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adp_restraints/adp_similarity_bpl.cpp g++ -o cctbx/adp_restraints/isotropic_adp.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adp_restraints/isotropic_adp.cpp g++ -o cctbx/adp_restraints/isotropic_adp_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adp_restraints/isotropic_adp_bpl.cpp g++ -o cctbx/adp_restraints/rigid_bond.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adp_restraints/rigid_bond.cpp g++ -o cctbx/adp_restraints/rigid_bond_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adp_restraints/rigid_bond_bpl.cpp g++ -o cctbx/adptbx/boost_python/adptbx_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/adptbx/boost_python/adptbx_ext.cpp g++ -o cctbx/array_family/boost_python/flex_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/array_family/boost_python/flex_ext.cpp g++ -o cctbx/array_family/boost_python/flex_hendrickson_lattman.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/array_family/boost_python/flex_miller_index.cpp g++ -o cctbx/array_family/boost_python/flex_xray_scatterer.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/array_family/boost_python/flex_xray_scatterer.cpp g++ -o cctbx/boost_python/emma_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/boost_python/orientation_ext.cpp g++ -o cctbx/boost_python/statistics_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/boost_python/statistics_ext.cpp g++ -o cctbx/crystal/asu_clusters_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/crystal/asu_clusters_bpl.cpp g++ -o cctbx/crystal/close_packing_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/crystal/close_packing_bpl.cpp g++ -o cctbx/crystal/coordination_sequences_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/crystal/coordination_sequences_bpl.cpp g++ -o cctbx/crystal/crystal_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/geometry_restraints/angle_bpl.cpp g++ -o cctbx/geometry_restraints/bond_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/geometry_restraints/bond_bpl.cpp g++ -o cctbx/geometry_restraints/bond_similarity_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/geometry_restraints/bond_sorted_bpl.cpp g++ -o cctbx/geometry_restraints/chirality_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/geometry_restraints/chirality_bpl.cpp g++ -o cctbx/geometry_restraints/dihedral_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/geometry_restraints/geometry_restraints_ext.cpp g++ -o cctbx/geometry_restraints/motif_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/geometry_restraints/motif_bpl.cpp g++ -o cctbx/geometry_restraints/nonbonded_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/maptbx/boost_python/gridding.cpp g++ -o cctbx/maptbx/boost_python/mapper.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/maptbx/boost_python/mapper.cpp g++ -o cctbx/maptbx/boost_python/maptbx_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/maptbx/boost_python/misc.cpp g++ -o cctbx/maptbx/boost_python/peak_search.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/maptbx/boost_python/peak_search.cpp g++ -o cctbx/maptbx/boost_python/pymol_interface.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math 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-fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/space_group_type.cpp g++ -o cctbx/sgtbx/symbols.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/symbols.cpp g++ -o cctbx/sgtbx/tensor_rank_2.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/tensor_rank_2.cpp g++ -o cctbx/sgtbx/tr_group.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/tr_group.cpp g++ -o cctbx/sgtbx/tr_vec.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/tr_vec.cpp g++ -o cctbx/sgtbx/utils.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/utils.cpp g++ -o cctbx/sgtbx/wyckoff.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/wyckoff.cpp g++ -o cctbx/sgtbx/reference_settings/hall_symbol_table.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/reference_settings/hall_symbol_table.cpp g++ -o cctbx/sgtbx/reference_settings/matrix_group_code_table.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/reference_settings/matrix_group_code_table.cpp g++ -o cctbx/sgtbx/reference_settings/normalizer.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/reference_settings/normalizer.cpp g++ -o cctbx/sgtbx/reference_settings/wyckoff.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/reference_settings/wyckoff.cpp g++ -o cctbx/uctbx/uctbx.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/uctbx/uctbx.cpp g++ -o cctbx/uctbx/spoil_optimization.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/uctbx/spoil_optimization.cpp g++ -o cctbx/uctbx/crystal_orientation.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/uctbx/crystal_orientation.cpp g++ -o cctbx/miller/boost_python/amplitude_normalisation.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/amplitude_normalisation.cpp g++ -o cctbx/miller/boost_python/asu.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/asu.cpp g++ -o cctbx/miller/boost_python/bins.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/bins.cpp g++ -o cctbx/miller/boost_python/change_basis.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/change_basis.cpp g++ -o cctbx/miller/boost_python/expand_to_p1.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/expand_to_p1.cpp g++ -o cctbx/miller/boost_python/f_calc_map.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/f_calc_map.cpp g++ -o cctbx/miller/boost_python/index_generator.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/index_generator.cpp g++ -o lib/libcctbx.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libcctbx.so.0.0 cctbx/eltbx/basic.o cctbx/eltbx/xray_scattering/it1992.o cctbx/eltbx/xray_scattering/wk1995.o cctbx/eltbx/xray_scattering/n_gaussian_raw.o cctbx/eltbx/xray_scattering/n_gaussian.o cctbx/eltbx/fp_fdp.o cctbx/eltbx/henke.o cctbx/eltbx/henke_tables_01_12.o cctbx/eltbx/henke_tables_13_24.o cctbx/eltbx/henke_tables_25_36.o cctbx/eltbx/henke_tables_37_48.o cctbx/eltbx/henke_tables_49_60.o cctbx/eltbx/henke_tables_61_72.o cctbx/eltbx/henke_tables_73_84.o cctbx/eltbx/henke_tables_85_92.o cctbx/eltbx/icsd_radii.o cctbx/eltbx/covalent_radii.o cctbx/eltbx/neutron.o cctbx/eltbx/sasaki.o cctbx/eltbx/sasaki_tables_01_12.o cctbx/eltbx/sasaki_tables_13_24.o cctbx/eltbx/sasaki_tables_25_36.o cctbx/eltbx/sasaki_tables_37_48.o cctbx/eltbx/sasaki_tables_49_60.o cctbx/eltbx/sasaki_tables_61_72.o cctbx/eltbx/sasaki_tables_73_82.o cctbx/eltbx/tiny_pse.o cctbx/eltbx/wavelengths.o cctbx/miller/asu.o cctbx/miller/bins.o cctbx/miller/index_generator.o cctbx/miller/index_span.o cctbx/miller/match_bijvoet_mates.o cctbx/miller/match_indices.o cctbx/miller/sym_equiv.o cctbx/sgtbx/bricks.o cctbx/sgtbx/change_of_basis_op.o cctbx/sgtbx/find_affine.o cctbx/sgtbx/group_codes.o cctbx/sgtbx/hall_in.o cctbx/sgtbx/lattice_tr.o cctbx/sgtbx/lattice_symmetry.o cctbx/sgtbx/miller.o cctbx/sgtbx/reciprocal_space_asu.o cctbx/sgtbx/reciprocal_space_ref_asu.o cctbx/sgtbx/rot_mx.o cctbx/sgtbx/rot_mx_info.o cctbx/sgtbx/row_echelon_solve.o cctbx/sgtbx/rt_mx.o cctbx/sgtbx/select_generators.o cctbx/sgtbx/seminvariant.o cctbx/sgtbx/site_symmetry.o cctbx/sgtbx/space_group.o cctbx/sgtbx/space_group_type.o cctbx/sgtbx/symbols.o cctbx/sgtbx/tensor_rank_2.o cctbx/sgtbx/tr_group.o cctbx/sgtbx/tr_vec.o cctbx/sgtbx/utils.o cctbx/sgtbx/wyckoff.o cctbx/sgtbx/reference_settings/hall_symbol_table.o cctbx/sgtbx/reference_settings/matrix_group_code_table.o cctbx/sgtbx/reference_settings/normalizer.o cctbx/sgtbx/reference_settings/wyckoff.o cctbx/uctbx/uctbx.o cctbx/uctbx/spoil_optimization.o cctbx/uctbx/crystal_orientation.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib 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-DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/lookup_utils.cpp g++ -o cctbx/miller/boost_python/match_bijvoet_mates.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include 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-DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/merge_equivalents.cpp g++ -o cctbx/miller/boost_python/miller_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include 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-I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/miller/boost_python/sym_equiv.cpp g++ -o cctbx/sgtbx/boost_python/brick.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/brick.cpp g++ -o cctbx/sgtbx/boost_python/change_of_basis.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC 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-I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/find_affine.cpp g++ -o cctbx/sgtbx/boost_python/lattice_symmetry.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/lattice_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/phase_info.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/reciprocal_space_asu.cpp g++ -o cctbx/sgtbx/boost_python/rot_mx.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/rot_mx.cpp g++ -o cctbx/sgtbx/boost_python/rt_mx.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/search_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/select_generators.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/select_generators.cpp g++ -o cctbx/sgtbx/boost_python/seminvariant.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/sgtbx_ext.cpp g++ -o cctbx/sgtbx/boost_python/site_symmetry.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/site_symmetry.cpp g++ -o cctbx/sgtbx/boost_python/space_group.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/space_group_type.cpp g++ -o cctbx/sgtbx/boost_python/sym_equiv_sites.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/sgtbx/boost_python/sym_equiv_sites.cpp g++ -o cctbx/sgtbx/boost_python/symbols.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math 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-I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/conversions.cpp g++ -o cctbx/xray/boost_python/curvatures_simple.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/curvatures_simple.cpp g++ -o cctbx/xray/boost_python/f_model_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/grouped_data.cpp g++ -o cctbx/xray/boost_python/minimization.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/minimization.cpp g++ -o cctbx/xray/boost_python/sampled_model_density.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/sampling_base.cpp g++ -o cctbx/xray/boost_python/scatterer.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/scatterer.cpp g++ -o cctbx/xray/boost_python/scatterer_flags.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/scattering_type_registry.cpp g++ -o cctbx/xray/boost_python/structure_factors_direct.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/structure_factors_direct.cpp g++ -o cctbx/xray/boost_python/structure_factors_simple.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/targets.cpp g++ -o cctbx/xray/boost_python/twin_targets.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/xray/boost_python/twin_targets.cpp g++ -o cctbx/xray/boost_python/xray_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB 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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/detectors/bruker_ext.cpp g++ -o iotbx/detectors/detectors_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/detectors/detectors_ext.cpp g++ -o lib/libcctbx_sgtbx_asu.so -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -shared cctbx/sgtbx/direct_space_asu/proto/cut.o 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-I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_ext.cpp g++ -o iotbx/pdb/hierarchy_select.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_select.cpp g++ -o iotbx/pdb/hierarchy_write.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_write.cpp g++ -o iotbx/pdb/hybrid_36_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hybrid_36_bpl.cpp gcc -o iotbx/pdb/hybrid_36_c.o -c -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hybrid_36_c.c g++ -o iotbx/pdb/hybrid_36_cpp.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hybrid_36_cpp.cpp g++ -o iotbx/pdb/input.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/input.cpp g++ -o iotbx/pdb/input_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/input_bpl.cpp g++ -o iotbx/pdb/input_write.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/input_write.cpp g++ -o iotbx/pdb/overall_counts.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/overall_counts.cpp g++ -o iotbx/pdb/rna_dna_atom_names_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/rna_dna_atom_names_bpl.cpp g++ -o iotbx/pdb/utils.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/utils.cpp g++ -o iotbx/pdb/write_utils.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/write_utils.cpp g++ -o iotbx/pdb/xray_structure_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/xray_structure_bpl.cpp g++ -o iotbx/shelx/shelx_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/shelx/shelx_ext.cpp g++ -o iotbx/wildcard_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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/iotbx/wildcard_ext.cpp g++ -o iotbx/xplor/boost_python/xplor_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/ccp4io/lib/src -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/xplor/boost_python/xplor_ext.cpp g++ -o lib/boost_adaptbx_python_streambuf_test_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp boost_adaptbx/tests/python_streambuf_test_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/boost_optional_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp boost_adaptbx/optional_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/boost_python_hybrid_times_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp boost_adaptbx/hybrid_times_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/boost_python_meta_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp boost_adaptbx/meta_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/boost_rational_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp boost_adaptbx/rational_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/boost_tuple_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp boost_adaptbx/tuple_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o scitbx/boost_python/utils.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/boost_python/utils.cpp g++ -o scitbx/boost_python/slice.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/boost_python/slice.cpp g++ -o scitbx/array_family/boost_python/utils.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/utils.cpp g++ -o omptbx/stubs.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/omptbx/stubs.cpp g++ -o lib/libomptbx.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libomptbx.so.0.0 omptbx/stubs.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib g++ -o lib/fable_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp fable/ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/libccp4io.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libccp4io.so.0.0 ccp4io_adaptbx/csymlib.o ccp4io/lib/src/library_err.o ccp4io/lib/src/library_file.o ccp4io/lib/src/library_utils.o ccp4io/lib/src/ccp4_array.o ccp4io/lib/src/ccp4_parser.o ccp4io/lib/src/ccp4_unitcell.o ccp4io/lib/src/cvecmat.o ccp4io/lib/src/cmtzlib.o ccp4io/lib/src/cmap_accessor.o ccp4io/lib/src/cmap_close.o ccp4io/lib/src/cmap_data.o ccp4io/lib/src/cmap_header.o ccp4io/lib/src/cmap_labels.o ccp4io/lib/src/cmap_open.o ccp4io/lib/src/cmap_skew.o ccp4io/lib/src/cmap_stats.o ccp4io/lib/src/cmap_symop.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lm g++ -o lib/iotbx_detectors_bruker_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/detectors/bruker_ext.o iotbx/detectors/bruker.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/iotbx_ccp4_map_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/ccp4_map/ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lccp4io -lboost_python-2.7 -lm g++ -o lib/iotbx_detectors_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/detectors/detectors_ext.o iotbx/detectors/image_divider.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/iotbx_dtrek_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/misc/boost_python/dtrek_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lboost_python-2.7 -lm g++ -o lib/libiotbx_mtz.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libiotbx_mtz.so.0.0 iotbx/mtz/object.o iotbx/mtz/crystal.o iotbx/mtz/dataset.o iotbx/mtz/column.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lccp4io -lm g++ -o lib/libiotbx_pdb.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libiotbx_pdb.so.0.0 iotbx/pdb/hybrid_36_c.o iotbx/pdb/hybrid_36_cpp.o iotbx/pdb/utils.o iotbx/pdb/write_utils.o iotbx/pdb/hierarchy.o iotbx/pdb/hierarchy_select.o iotbx/pdb/hierarchy_atoms.o iotbx/pdb/construct_hierarchy.o iotbx/pdb/overall_counts.o iotbx/pdb/hierarchy_write.o iotbx/pdb/atom_selection.o iotbx/pdb/input.o iotbx/pdb/input_write.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib g++ -o lib/iotbx_scalepack_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/misc/boost_python/scalepack_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lboost_python-2.7 -lm g++ -o mmtbx/masks/atom_mask.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/masks/atom_mask.cpp g++ -o lib/iotbx_wildcard_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/wildcard_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o rstbx/dps_core/dps_core.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/dps_core/dps_core.cpp g++ -o rstbx/dps_core/directional_fft.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/dps_core/directional_fft.cpp g++ -o lib/libscitbx_boost_python.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libscitbx_boost_python.so.0.0 scitbx/boost_python/utils.o scitbx/boost_python/slice.o scitbx/array_family/boost_python/utils.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 g++ -o lib/cctbx_eltbx_sasaki_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/sasaki_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_adptbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/adptbx/boost_python/adptbx_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_geometry_restraints_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/geometry_restraints/geometry_restraints_ext.o cctbx/geometry_restraints/bond_bpl.o cctbx/geometry_restraints/bond_similarity_bpl.o cctbx/geometry_restraints/bond_sorted_bpl.o cctbx/geometry_restraints/nonbonded_bpl.o cctbx/geometry_restraints/nonbonded_sorted_bpl.o cctbx/geometry_restraints/angle_bpl.o cctbx/geometry_restraints/dihedral_bpl.o cctbx/geometry_restraints/chirality_bpl.o cctbx/geometry_restraints/planarity_bpl.o cctbx/geometry_restraints/motif_bpl.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/iotbx_pdb_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/pdb/ext.o iotbx/pdb/hybrid_36_bpl.o iotbx/pdb/common_residue_names_bpl.o iotbx/pdb/rna_dna_atom_names_bpl.o iotbx/pdb/input_bpl.o iotbx/pdb/xray_structure_bpl.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_masks_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/masks/boost_python/masks_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_eltbx_xray_scattering_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/xray_scattering_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_sgtbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/sgtbx/boost_python/sgtbx_ext.o cctbx/sgtbx/boost_python/brick.o cctbx/sgtbx/boost_python/change_of_basis.o cctbx/sgtbx/boost_python/find_affine.o cctbx/sgtbx/boost_python/lattice_symmetry.o cctbx/sgtbx/boost_python/phase_info.o cctbx/sgtbx/boost_python/reciprocal_space_asu.o cctbx/sgtbx/boost_python/rot_mx.o cctbx/sgtbx/boost_python/rt_mx.o cctbx/sgtbx/boost_python/search_symmetry.o cctbx/sgtbx/boost_python/seminvariant.o cctbx/sgtbx/boost_python/site_symmetry.o cctbx/sgtbx/boost_python/space_group.o cctbx/sgtbx/boost_python/space_group_type.o cctbx/sgtbx/boost_python/sym_equiv_sites.o cctbx/sgtbx/boost_python/symbols.o cctbx/sgtbx/boost_python/tensor_rank_2.o cctbx/sgtbx/boost_python/tr_vec.o cctbx/sgtbx/boost_python/wyckoff.o cctbx/sgtbx/boost_python/select_generators.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_translation_search_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/translation_search/boost_python/translation_search_ext.o cctbx/translation_search/boost_python/fast_nv1995.o cctbx/translation_search/boost_python/fast_terms.o cctbx/translation_search/boost_python/symmetry_flags.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_math_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/math/boost_python/math_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_miller_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/miller/boost_python/miller_ext.o cctbx/miller/boost_python/asu.o cctbx/miller/boost_python/bins.o cctbx/miller/boost_python/change_basis.o cctbx/miller/boost_python/expand_to_p1.o cctbx/miller/boost_python/index_generator.o cctbx/miller/boost_python/index_span.o cctbx/miller/boost_python/match_bijvoet_mates.o cctbx/miller/boost_python/match_indices.o cctbx/miller/boost_python/merge_equivalents.o cctbx/miller/boost_python/phase_integrator.o cctbx/miller/boost_python/phase_transfer.o cctbx/miller/boost_python/sym_equiv.o cctbx/miller/boost_python/f_calc_map.o cctbx/miller/boost_python/lookup_utils.o cctbx/miller/boost_python/amplitude_normalisation.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_eltbx_fp_fdp_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/fp_fdp_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_eltbx_covalent_radii_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp 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-Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/chemical_elements_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_crystal_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/crystal/crystal_ext.o cctbx/crystal/asu_clusters_bpl.o cctbx/crystal/close_packing_bpl.o cctbx/crystal/coordination_sequences_bpl.o cctbx/crystal/direct_space_asu_bpl.o cctbx/crystal/incremental_pairs_bpl.o cctbx/crystal/neighbors_bpl.o cctbx/crystal/pair_tables_bpl.o cctbx/crystal/site_cluster_analysis_bpl.o cctbx/crystal/symmetry_bpl.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_eltbx_tiny_pse_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/tiny_pse_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_xray_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/xray/boost_python/xray_ext.o cctbx/xray/boost_python/conversions.o cctbx/xray/boost_python/gradient_flags.o cctbx/xray/boost_python/gradients_direct.o cctbx/xray/boost_python/fast_gradients.o cctbx/xray/boost_python/minimization.o cctbx/xray/boost_python/scatterer_flags.o cctbx/xray/boost_python/scatterer.o cctbx/xray/boost_python/scattering_type_registry.o cctbx/xray/boost_python/sampling_base.o cctbx/xray/boost_python/sampled_model_density.o cctbx/xray/boost_python/structure_factors_direct.o cctbx/xray/boost_python/structure_factors_simple.o cctbx/xray/boost_python/curvatures_simple.o cctbx/xray/boost_python/targets.o cctbx/xray/boost_python/f_model_bpl.o cctbx/xray/boost_python/twin_targets.o cctbx/xray/boost_python/grouped_data.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_adp_restraints_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/adp_restraints/adp_restraints_ext.o cctbx/adp_restraints/rigid_bond_bpl.o cctbx/adp_restraints/rigid_bond.o cctbx/adp_restraints/adp_similarity_bpl.o cctbx/adp_restraints/adp_similarity.o cctbx/adp_restraints/isotropic_adp_bpl.o cctbx/adp_restraints/isotropic_adp.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_eltbx_henke_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/henke_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/iotbx_mtz_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/mtz/ext.o iotbx/mtz/object_bpl.o iotbx/mtz/crystal_bpl.o iotbx/mtz/dataset_bpl.o iotbx/mtz/column_bpl.o iotbx/mtz/batch_bpl.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -liotbx_mtz -lcctbx -lccp4io -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_dmtbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/dmtbx/boost_python/dmtbx_ext.o cctbx/dmtbx/boost_python/triplet_phase_relation.o cctbx/dmtbx/boost_python/triplet_generator.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/iotbx_shelx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/shelx/shelx_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lboost_python-2.7 -lm g++ -o lib/fftw3tbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp fftw3tbx/ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lfftw3 -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_statistics_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/boost_python/statistics_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_eltbx_icsd_radii_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/icsd_radii_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/cctbx_uctbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/uctbx/boost_python/uctbx_ext.o cctbx/uctbx/boost_python/fast_minimum_reduction.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/iotbx_xplor_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/xplor/boost_python/xplor_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lboost_python-2.7 -lm g++ -o lib/cctbx_orientation_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/boost_python/orientation_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o rstbx/dps_core/direction.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/dps_core/direction.cpp g++ -o rstbx/diffraction/ewald_sphere.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/diffraction/ewald_sphere.cpp g++ -o scitbx/minpack/raw.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/minpack/raw.cpp gcc -o scitbx/slatec/lib_c.o -c -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/slatec/lib_c.c g++ -o mmtbx/alignment_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/alignment_ext.cpp g++ -o mmtbx/bulk_solvent/bulk_solvent_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent_ext.cpp g++ -o lib/libscitbx_slatec.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libscitbx_slatec.so.0.0 scitbx/slatec/lib_c.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lm g++ -o mmtbx/bulk_solvent/bulk_solvent.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.cpp g++ -o lib/libscitbx_minpack.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,libscitbx_minipack.so.0.0 scitbx/minpack/raw.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lm g++ -o mmtbx/dynamics/dynamics_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/dynamics/dynamics_ext.cpp g++ -o mmtbx/dynamics/dynamics.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/dynamics/dynamics.cpp g++ -o lib/librstbx.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp -Wl,-soname,librstbx.so.0.0 rstbx/dps_core/dps_core.o rstbx/dps_core/directional_fft.o rstbx/dps_core/direction.o rstbx/diffraction/ewald_sphere.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lm g++ -o mmtbx/f_model/f_model_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/f_model/f_model_ext.cpp g++ -o lib/iotbx_pdb_hierarchy_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp iotbx/pdb/hierarchy_ext.o iotbx/pdb/hierarchy_atom_bpl.o iotbx/pdb/hierarchy_atoms_bpl.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/masks/masks_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/masks/masks_ext.cpp g++ -o mmtbx/max_lik/max_lik_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/max_lik/max_lik_ext.cpp g++ -o mmtbx/max_lik/max_lik.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/max_lik/max_lik.cpp g++ -o lib/mmtbx_alignment_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/alignment_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/ncs/restraints_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/ncs/restraints_ext.cpp g++ -o lib/libmmtbx_masks.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/masks/atom_mask.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lomptbx -lm g++ -o mmtbx/rsr/rsr_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/rsr/rsr_ext.cpp g++ -o lib/mmtbx_dynamics_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/dynamics/dynamics_ext.o mmtbx/dynamics/dynamics.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/scaling/scaling_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/scaling/scaling_ext.cpp g++ -o lib/mmtbx_bulk_solvent_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/bulk_solvent/bulk_solvent_ext.o mmtbx/bulk_solvent/bulk_solvent.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/scaling/twinning_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/scaling/twinning_bpl.cpp g++ -o lib/mmtbx_f_model_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/f_model/f_model_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/scaling/relative_scaling_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/scaling/relative_scaling_bpl.cpp g++ -o lib/mmtbx_masks_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/masks/masks_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lmmtbx_masks -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/scaling/outlier_bpl.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/scaling/outlier_bpl.cpp g++ -o mmtbx/tls/tls_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/tls/tls_ext.cpp g++ -o lib/mmtbx_ncs_restraints_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/ncs/restraints_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o mmtbx/utils/utils_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/mmtbx/utils/utils_ext.cpp g++ -o lib/mmtbx_rsr_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/rsr/rsr_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o omptbx/ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/omptbx/ext.cpp g++ -o lib/mmtbx_max_lik_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/max_lik/max_lik_ext.o mmtbx/max_lik/max_lik.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o rstbx/array_family/ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/array_family/ext.cpp g++ -o rstbx/array_family/flex_rstbx_arrays.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/array_family/flex_rstbx_arrays.cpp g++ -o rstbx/ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/usr/include/python2.7 -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 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/rstbx/ext.cpp g++ -o lib/omptbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp omptbx/ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lomptbx -lboost_python-2.7 -lm g++ -o scitbx/array_family/boost_python/flex_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_ext.cpp g++ -o lib/mmtbx_utils_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/utils/utils_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/array_family/boost_python/flex_grid.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_grid.cpp g++ -o scitbx/array_family/boost_python/flex_bool.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_bool.cpp g++ -o scitbx/array_family/boost_python/flex_size_t.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_size_t.cpp g++ -o lib/mmtbx_scaling_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/scaling/scaling_ext.o mmtbx/scaling/twinning_bpl.o mmtbx/scaling/relative_scaling_bpl.o mmtbx/scaling/outlier_bpl.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/array_family/boost_python/flex_int.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_int.cpp g++ -o lib/mmtbx_tls_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp mmtbx/tls/tls_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/array_family/boost_python/flex_long.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_long.cpp g++ -o lib/rstbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp rstbx/ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lrstbx -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/array_family/boost_python/flex_float.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_float.cpp g++ -o scitbx/array_family/boost_python/flex_double.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_double.cpp g++ -o scitbx/array_family/boost_python/flex_double_matrix.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_double_matrix.cpp g++ -o scitbx/array_family/boost_python/flex_complex_double.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_complex_double.cpp g++ -o lib/rstbx_array_family_flex_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp rstbx/array_family/ext.o rstbx/array_family/flex_rstbx_arrays.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lrstbx -lcctbx -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/array_family/boost_python/flex_std_string.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_std_string.cpp g++ -o scitbx/array_family/boost_python/flex_random.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_random.cpp g++ -o scitbx/array_family/boost_python/flex_sort.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_sort.cpp g++ -o scitbx/array_family/boost_python/flex_histogram.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_histogram.cpp g++ -o scitbx/array_family/boost_python/flex_mean_and_variance.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_mean_and_variance.cpp g++ -o scitbx/array_family/boost_python/flex_median.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_median.cpp g++ -o scitbx/array_family/boost_python/flex_linear_interpolation.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_linear_interpolation.cpp g++ -o scitbx/array_family/boost_python/flex_vec3_double.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_vec3_double.cpp g++ -o scitbx/array_family/boost_python/flex_vec2_double.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_vec2_double.cpp g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp g++ -o scitbx/array_family/boost_python/loops.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/loops.cpp g++ -o scitbx/array_family/boost_python/show_sizes.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/show_sizes.cpp g++ -o scitbx/array_family/boost_python/shared_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/array_family/boost_python/shared_ext.cpp g++ -o scitbx/boost_python/slice_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/boost_python/slice_ext.cpp g++ -o lib/scitbx_boost_python_slice_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/boost_python/slice_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/fftpack/boost_python/fftpack_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/fftpack/boost_python/fftpack_ext.cpp g++ -o scitbx/iso_surface/iso_surface_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/iso_surface/iso_surface_ext.cpp g++ -o scitbx/lbfgs/ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgs/ext.cpp g++ -o scitbx/lbfgsb/boost_python/lbfgsb_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp g++ -o scitbx/linalg/boost_python/linalg_ext.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/linalg/boost_python/linalg_ext.cpp g++ -o scitbx/linalg/boost_python/matrix.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/linalg/boost_python/matrix.cpp g++ -o scitbx/linalg/boost_python/cholesky.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/linalg/boost_python/cholesky.cpp g++ -o lib/scitbx_array_family_flex_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/array_family/boost_python/flex_ext.o scitbx/array_family/boost_python/flex_grid.o scitbx/array_family/boost_python/flex_bool.o scitbx/array_family/boost_python/flex_size_t.o scitbx/array_family/boost_python/flex_int.o scitbx/array_family/boost_python/flex_long.o scitbx/array_family/boost_python/flex_float.o scitbx/array_family/boost_python/flex_double.o scitbx/array_family/boost_python/flex_double_matrix.o scitbx/array_family/boost_python/flex_complex_double.o scitbx/array_family/boost_python/flex_std_string.o scitbx/array_family/boost_python/flex_random.o scitbx/array_family/boost_python/flex_sort.o scitbx/array_family/boost_python/flex_histogram.o scitbx/array_family/boost_python/flex_mean_and_variance.o scitbx/array_family/boost_python/flex_median.o scitbx/array_family/boost_python/flex_linear_interpolation.o scitbx/array_family/boost_python/flex_vec3_double.o scitbx/array_family/boost_python/flex_vec2_double.o scitbx/array_family/boost_python/flex_sym_mat3_double.o scitbx/array_family/boost_python/flex_tiny_size_t_2.o scitbx/array_family/boost_python/loops.o scitbx/array_family/boost_python/show_sizes.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o lib/scitbx_iso_surface_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/iso_surface/iso_surface_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lscitbx_boost_python -lboost_python-2.7 -lm g++ -o scitbx/linalg/boost_python/householder.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/linalg/boost_python/householder.cpp g++ -o scitbx/linalg/boost_python/svd.o -c -march=native -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6 -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -Wformat -Werror=format-security -g0 -O2 -fopenmp -Iinclude -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/include -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources -I/usr/include/python2.7 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/linalg/boost_python/svd.cpp In file included from /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb.h:8:0, from /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp:3: /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h: In instantiation of 'void scitbx::lbfgsb::raw::mainlb(const int&, const int&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, FloatType&, const scitbx::lbfgsb::raw::ref1&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, bool) [with FloatType = double; std::string = std::basic_string]': /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:4457:22: required from 'void scitbx::lbfgsb::raw::setulb(const int&, const int&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, FloatType&, const scitbx::lbfgsb::raw::ref1&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, bool) [with FloatType = double; std::string = std::basic_string]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb.h:161:29: required from 'bool scitbx::lbfgsb::minimizer::process(const scitbx::af::ref&, const FloatType&, const scitbx::af::ref&, bool) [with FloatType = double]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp:29:25: required from 'static void scitbx::lbfgsb::{anonymous}::minimizer_wrappers::wrap() [with FloatType = double]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp:112:33: required from here /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:3905:38: error: format not a string literal and no format arguments [-Werror=format-security] if(iprint >= 1) printf(fmt_1005); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:3971:39: error: format not a string literal and no format arguments [-Werror=format-security] if(iprint >= 1) printf(fmt_1005); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h: In instantiation of 'void scitbx::lbfgsb::raw::prn3lb(const int&, const scitbx::lbfgsb::raw::ref1&, const FloatType&, const string&, const int&, const int&, const int&, const int&, const int&, const int&, const int&, const int&, const FloatType&, const FloatType&, const int&, const string&, const int&, const FloatType&, const FloatType&, const int&, const FloatType&, const FloatType&, const FloatType&) [with FloatType = double; std::string = std::basic_string]': /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:3789:36: required from 'void scitbx::lbfgsb::raw::mainlb(const int&, const int&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, FloatType&, const scitbx::lbfgsb::raw::ref1&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref2&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, bool) [with FloatType = double; std::string = std::basic_string]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:4457:22: required from 'void scitbx::lbfgsb::raw::setulb(const int&, const int&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, FloatType&, const scitbx::lbfgsb::raw::ref1&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, const scitbx::lbfgsb::raw::ref1&, bool) [with FloatType = double; std::string = std::basic_string]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb.h:161:29: required from 'bool scitbx::lbfgsb::minimizer::process(const scitbx::af::ref&, const FloatType&, const scitbx::af::ref&, bool) [with FloatType = double]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp:29:25: required from 'static void scitbx::lbfgsb::{anonymous}::minimizer_wrappers::wrap() [with FloatType = double]' /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/boost_python/lbfgsb_ext.cpp:112:33: required from here /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:970:22: error: format not a string literal and no format arguments [-Werror=format-security] printf(fmt_3003); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:971:22: error: format not a string literal and no format arguments [-Werror=format-security] printf(fmt_3004); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:982:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -1) printf(fmt_9011); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:983:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -2) printf(fmt_9012); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:984:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -3) printf(fmt_9013); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:985:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -4) printf(fmt_9014); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:986:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -5) printf(fmt_9015); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:993:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -8) printf(fmt_9018); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:994:40: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -9) printf(fmt_9019); ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1005:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -1) printf(fmt_9011); // itfile ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1006:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -2) printf(fmt_9012); // itfile ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1007:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -3) printf(fmt_9013); // itfile ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1008:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -4) printf(fmt_9014); // itfile ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1009:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -5) printf(fmt_9015); // itfile ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1010:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -8) printf(fmt_9018); // itfile ^ /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:1011:42: error: format not a string literal and no format arguments [-Werror=format-security] if (info == -9) printf(fmt_9019); // itfile ^ cc1plus: some warnings being treated as errors scons: *** [scitbx/lbfgsb/boost_python/lbfgsb_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 93: Called src_compile * environment, line 3039: 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/log/build/sci-libs/cctbx-2010.03.29.2334-r7:20150419-124149.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'