cctbx-2010.03.29.2334-r7:20150806-073918.log

cctbx-2010.03.29.2334-r7:20150806-073918.log (text/plain), 269.23 KB, created by Agostino Sarubbo on 2015-08-06 09:54:07 UTC

 * Package:    sci-libs/cctbx-2010.03.29.2334-r7
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * 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 -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6
  CFLAGS =  -march=native -O2 -g0 -pipe -std=gnu11
  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: a4536fadf140b5db949260093e047dd9
  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
scons: Reading SConscript files ...
libtbx.scons: using flags from initial environment: 
              CXXFLAGS =  -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6
              CFLAGS =  -march=native -O2 -g0 -pipe -std=gnu11
              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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_restraints_ext.cpp
g++ -o cctbx/adp_restraints/adp_similarity.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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.cpp
g++ -o cctbx/adp_restraints/adp_similarity_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_hendrickson_lattman.cpp
g++ -o cctbx/array_family/boost_python/flex_miller_index.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_miller_index.cpp
g++ -o cctbx/array_family/boost_python/flex_xray_scatterer.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/emma_ext.cpp
g++ -o cctbx/boost_python/orientation_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/orientation_ext.cpp
g++ -o cctbx/boost_python/statistics_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/crystal_ext.cpp
g++ -o cctbx/crystal/direct_space_asu_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/direct_space_asu_bpl.cpp
g++ -o cctbx/crystal/incremental_pairs_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/incremental_pairs_bpl.cpp
g++ -o cctbx/crystal/neighbors_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/neighbors_bpl.cpp
g++ -o cctbx/crystal/pair_tables_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/pair_tables_bpl.cpp
g++ -o cctbx/crystal/site_cluster_analysis_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/site_cluster_analysis_bpl.cpp
g++ -o cctbx/crystal/symmetry_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/symmetry_bpl.cpp
g++ -o cctbx/dmtbx/boost_python/dmtbx_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/dmtbx/boost_python/dmtbx_ext.cpp
g++ -o cctbx/dmtbx/boost_python/triplet_generator.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/dmtbx/boost_python/triplet_generator.cpp
g++ -o cctbx/dmtbx/boost_python/triplet_phase_relation.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/dmtbx/boost_python/triplet_phase_relation.cpp
g++ -o cctbx/eltbx/basic.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/basic.cpp
g++ -o cctbx/eltbx/boost_python/chemical_elements_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/chemical_elements_ext.cpp
g++ -o cctbx/eltbx/boost_python/covalent_radii_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/covalent_radii_ext.cpp
g++ -o cctbx/eltbx/boost_python/fp_fdp_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/fp_fdp_ext.cpp
g++ -o cctbx/eltbx/boost_python/henke_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/henke_ext.cpp
g++ -o cctbx/eltbx/boost_python/icsd_radii_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/icsd_radii_ext.cpp
g++ -o cctbx/eltbx/boost_python/neutron_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/neutron_ext.cpp
g++ -o cctbx/eltbx/boost_python/sasaki_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/sasaki_ext.cpp
g++ -o cctbx/eltbx/boost_python/tiny_pse_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/tiny_pse_ext.cpp
g++ -o cctbx/eltbx/boost_python/wavelengths_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/wavelengths_ext.cpp
g++ -o cctbx/eltbx/boost_python/xray_scattering_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/boost_python/xray_scattering_ext.cpp
g++ -o cctbx/eltbx/covalent_radii.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/covalent_radii.cpp
g++ -o cctbx/eltbx/fp_fdp.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/fp_fdp.cpp
g++ -o cctbx/eltbx/henke.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke.cpp
g++ -o cctbx/eltbx/henke_tables_01_12.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_01_12.cpp
g++ -o cctbx/eltbx/henke_tables_13_24.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_13_24.cpp
g++ -o cctbx/eltbx/henke_tables_25_36.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_25_36.cpp
g++ -o cctbx/eltbx/henke_tables_37_48.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_37_48.cpp
g++ -o cctbx/eltbx/henke_tables_49_60.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_49_60.cpp
g++ -o cctbx/eltbx/henke_tables_61_72.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_61_72.cpp
g++ -o cctbx/eltbx/henke_tables_73_84.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_73_84.cpp
g++ -o cctbx/eltbx/henke_tables_85_92.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/henke_tables_85_92.cpp
g++ -o cctbx/eltbx/icsd_radii.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/icsd_radii.cpp
g++ -o cctbx/eltbx/neutron.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/neutron.cpp
g++ -o cctbx/eltbx/sasaki.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki.cpp
g++ -o cctbx/eltbx/sasaki_tables_01_12.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_01_12.cpp
g++ -o cctbx/eltbx/sasaki_tables_13_24.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_13_24.cpp
g++ -o cctbx/eltbx/sasaki_tables_25_36.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_25_36.cpp
g++ -o cctbx/eltbx/sasaki_tables_37_48.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_37_48.cpp
g++ -o cctbx/eltbx/sasaki_tables_49_60.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_49_60.cpp
g++ -o cctbx/eltbx/sasaki_tables_61_72.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_61_72.cpp
g++ -o cctbx/eltbx/sasaki_tables_73_82.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 cctbx/eltbx/sasaki_tables_73_82.cpp
g++ -o cctbx/eltbx/tiny_pse.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/tiny_pse.cpp
g++ -o cctbx/eltbx/wavelengths.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/wavelengths.cpp
g++ -o cctbx/eltbx/xray_scattering/it1992.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/xray_scattering/it1992.cpp
g++ -o cctbx/eltbx/xray_scattering/n_gaussian.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/xray_scattering/n_gaussian.cpp
g++ -o cctbx/eltbx/xray_scattering/n_gaussian_raw.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/xray_scattering/n_gaussian_raw.cpp
g++ -o cctbx/eltbx/xray_scattering/wk1995.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eltbx/xray_scattering/wk1995.cpp
g++ -o cctbx/examples/convert_ccp4_symop_lib.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp -Icctbx/examples -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/examples -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/examples/convert_ccp4_symop_lib.cpp
g++ -o cctbx/examples/find_distances.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp -Icctbx/examples -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/examples -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/examples/find_distances.cpp
g++ -o cctbx/examples/getting_started.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp -Icctbx/examples -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/examples -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/examples/getting_started.cpp
g++ -o cctbx/examples/lattice_symmetry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp -Icctbx/examples -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/examples -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/examples/lattice_symmetry.cpp
g++ -o cctbx/examples/sym_equiv_sites.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp -Icctbx/examples -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/examples -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/examples/sym_equiv_sites.cpp
g++ -o cctbx/examples/sys_abs_equiv_space_groups.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp -Icctbx/examples -I/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/cctbx/examples -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/examples/sys_abs_equiv_space_groups.cpp
g++ -o cctbx/geometry_restraints/angle_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/angle_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/bond_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/bond_similarity_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_similarity_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/bond_sorted_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_sorted_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/chirality_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/dihedral_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/dihedral_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/geometry_restraints_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/geometry_restraints_ext.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/motif_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/nonbonded_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/nonbonded_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/nonbonded_sorted_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/nonbonded_sorted_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/geometry_restraints/planarity_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/planarity_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o cctbx/maptbx/boost_python/basic_map.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/basic_map.cpp
g++ -o cctbx/maptbx/boost_python/coordinate_transformers.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/coordinate_transformers.cpp
g++ -o cctbx/maptbx/boost_python/grid_indices_around_sites.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/grid_indices_around_sites.cpp
g++ -o cctbx/maptbx/boost_python/grid_tags.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/grid_tags.cpp
g++ -o cctbx/maptbx/boost_python/gridding.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/gridding.cpp
g++ -o cctbx/maptbx/boost_python/mapper.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/maptbx_ext.cpp
g++ -o cctbx/maptbx/boost_python/misc.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/misc.cpp
g++ -o cctbx/maptbx/boost_python/peak_search.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/pymol_interface.cpp
g++ -o cctbx/maptbx/boost_python/real_space_refinement.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/real_space_refinement.cpp
g++ -o cctbx/maptbx/boost_python/statistics.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/statistics.cpp
g++ -o cctbx/maptbx/boost_python/structure_factors.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/structure_factors.cpp
g++ -o cctbx/masks/boost_python/masks_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/masks/boost_python/masks_ext.cpp
g++ -o cctbx/math/boost_python/math_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/math_ext.cpp
g++ -o cctbx/math/time_trigonometry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/time_trigonometry.cpp
g++ -o cctbx/miller/asu.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/asu.cpp
g++ -o cctbx/miller/bins.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/bins.cpp
g++ -o cctbx/miller/index_generator.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/index_generator.cpp
g++ -o cctbx/miller/index_span.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/index_span.cpp
g++ -o cctbx/miller/match_bijvoet_mates.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/match_bijvoet_mates.cpp
g++ -o cctbx/miller/match_indices.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/match_indices.cpp
g++ -o cctbx/miller/sym_equiv.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller/sym_equiv.cpp
g++ -o cctbx/sgtbx/bricks.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/bricks.cpp
g++ -o cctbx/sgtbx/change_of_basis_op.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/change_of_basis_op.cpp
g++ -o cctbx/sgtbx/find_affine.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/find_affine.cpp
g++ -o cctbx/sgtbx/group_codes.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/group_codes.cpp
g++ -o cctbx/sgtbx/hall_in.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/hall_in.cpp
g++ -o cctbx/sgtbx/lattice_tr.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/lattice_tr.cpp
g++ -o cctbx/sgtbx/lattice_symmetry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/lattice_symmetry.cpp
g++ -o cctbx/sgtbx/miller.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller.cpp
g++ -o cctbx/sgtbx/reciprocal_space_asu.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/reciprocal_space_asu.cpp
g++ -o cctbx/sgtbx/reciprocal_space_ref_asu.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/reciprocal_space_ref_asu.cpp
g++ -o cctbx/sgtbx/rot_mx.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/rot_mx.cpp
g++ -o cctbx/sgtbx/rot_mx_info.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/rot_mx_info.cpp
g++ -o cctbx/sgtbx/row_echelon_solve.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/row_echelon_solve.cpp
g++ -o cctbx/sgtbx/rt_mx.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/rt_mx.cpp
g++ -o cctbx/sgtbx/select_generators.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/select_generators.cpp
g++ -o cctbx/sgtbx/seminvariant.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/seminvariant.cpp
g++ -o cctbx/sgtbx/site_symmetry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/site_symmetry.cpp
g++ -o cctbx/sgtbx/space_group.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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.cpp
g++ -o cctbx/sgtbx/space_group_type.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -lm
g++ -o cctbx/math/time_trigonometry -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/math/time_trigonometry.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lm
g++ -o cctbx/miller/boost_python/index_span.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_span.cpp
g++ -o cctbx/miller/boost_python/lookup_utils.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/match_bijvoet_mates.cpp
g++ -o cctbx/miller/boost_python/match_indices.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/match_indices.cpp
g++ -o cctbx/miller/boost_python/merge_equivalents.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/miller_ext.cpp
g++ -o cctbx/miller/boost_python/phase_integrator.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/phase_integrator.cpp
g++ -o cctbx/miller/boost_python/phase_transfer.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/phase_transfer.cpp
g++ -o cctbx/miller/boost_python/sym_equiv.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/sym_equiv.cpp
g++ -o cctbx/sgtbx/boost_python/brick.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/change_of_basis.cpp
g++ -o cctbx/sgtbx/boost_python/find_affine.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/find_affine.cpp
g++ -o cctbx/sgtbx/boost_python/lattice_symmetry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/phase_info.cpp
g++ -o cctbx/sgtbx/boost_python/reciprocal_space_asu.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/reciprocal_space_asu.cpp
g++ -o cctbx/sgtbx/boost_python/rot_mx.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/rt_mx.cpp
g++ -o cctbx/sgtbx/boost_python/search_symmetry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/search_symmetry.cpp
g++ -o cctbx/sgtbx/boost_python/select_generators.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/seminvariant.cpp
g++ -o cctbx/sgtbx/boost_python/sgtbx_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/sgtbx_ext.cpp
g++ -o cctbx/sgtbx/boost_python/site_symmetry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/space_group.cpp
g++ -o cctbx/sgtbx/boost_python/space_group_type.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/space_group_type.cpp
g++ -o cctbx/sgtbx/boost_python/sym_equiv_sites.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/symbols.cpp
g++ -o cctbx/sgtbx/boost_python/tensor_rank_2.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/tensor_rank_2.cpp
g++ -o cctbx/sgtbx/boost_python/tr_vec.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/tr_vec.cpp
g++ -o cctbx/sgtbx/boost_python/wyckoff.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/wyckoff.cpp
g++ -o cctbx/sgtbx/direct_space_asu/proto/asu_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/cctbx/sgtbx/direct_space_asu/proto/asu_ext.cpp
g++ -o cctbx/sgtbx/direct_space_asu/proto/cut.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/direct_space_asu/proto/cut.cpp
g++ -o cctbx/sgtbx/direct_space_asu/proto/direct_space_asu.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/direct_space_asu/proto/direct_space_asu.cpp
g++ -o cctbx/sgtbx/direct_space_asu/proto/reference_table.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/direct_space_asu/proto/reference_table.cpp
g++ -o cctbx/sgtbx/direct_space_asu/proto/tst_asu.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/direct_space_asu/proto/tst_asu.cpp
g++ -o cctbx/symmetry_search/boost_python/symmetry_search_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/symmetry_search/boost_python/symmetry_search_ext.cpp
g++ -o cctbx/translation_search/boost_python/fast_nv1995.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/translation_search/boost_python/fast_nv1995.cpp
g++ -o cctbx/translation_search/boost_python/fast_terms.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/translation_search/boost_python/fast_terms.cpp
g++ -o cctbx/translation_search/boost_python/symmetry_flags.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/translation_search/boost_python/symmetry_flags.cpp
g++ -o cctbx/translation_search/boost_python/translation_search_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/translation_search/boost_python/translation_search_ext.cpp
g++ -o cctbx/uctbx/boost_python/fast_minimum_reduction.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/uctbx/boost_python/fast_minimum_reduction.cpp
g++ -o cctbx/uctbx/boost_python/uctbx_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/uctbx/boost_python/uctbx_ext.cpp
g++ -o cctbx/xray/boost_python/conversions.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/conversions.cpp
g++ -o cctbx/xray/boost_python/curvatures_simple.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/f_model_bpl.cpp
g++ -o cctbx/xray/boost_python/fast_gradients.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/fast_gradients.cpp
g++ -o cctbx/xray/boost_python/gradient_flags.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/gradient_flags.cpp
g++ -o cctbx/xray/boost_python/gradients_direct.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/gradients_direct.cpp
g++ -o cctbx/xray/boost_python/grouped_data.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/grouped_data.cpp
g++ -o cctbx/xray/boost_python/minimization.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/sampled_model_density.cpp
g++ -o cctbx/xray/boost_python/sampling_base.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/sampling_base.cpp
g++ -o cctbx/xray/boost_python/scatterer.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_flags.cpp
g++ -o cctbx/xray/boost_python/scattering_type_registry.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/scattering_type_registry.cpp
g++ -o cctbx/xray/boost_python/structure_factors_direct.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_simple.cpp
g++ -o cctbx/xray/boost_python/targets.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/targets.cpp
g++ -o cctbx/xray/boost_python/twin_targets.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/xray_ext.cpp
g++ -o chiltbx/handle_test.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/chiltbx/handle_test.cpp
g++ -o clipper/examples/symtest.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/clipper/examples/symtest.cpp
g++ -o clipper_adaptbx/sanity_check.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -fopenmp /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp
g++ -o fable/ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/fable -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/fable/ext.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o chiltbx/handle_test -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp chiltbx/handle_test.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib
g++ -o exe_dev/clipper.sanity_check -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp clipper_adaptbx/sanity_check.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lm
g++ -o fftw3tbx/ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/fftw3tbx/ext.cpp
g++ -o iotbx/ccp4_map/ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/ccp4_map/ext.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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 cctbx/sgtbx/direct_space_asu/proto/reference_table.o cctbx/sgtbx/direct_space_asu/proto/direct_space_asu.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx -lm
g++ -o exe_dev/clipper.symtest -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp clipper/examples/symtest.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lm
g++ -o iotbx/detectors/bruker.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/bruker.cpp
g++ -o exe_dev/cctbx.getting_started -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/examples/getting_started.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/examples/convert_ccp4_symop_lib.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o exe_dev/cctbx.find_distances -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/examples/find_distances.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o exe_dev/cctbx.lattice_symmetry -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/examples/lattice_symmetry.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o exe_dev/cctbx.sym_equiv_sites -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/examples/sym_equiv_sites.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o cctbx/sgtbx/direct_space_asu/proto/tst_asu -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/sgtbx/direct_space_asu/proto/tst_asu.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o exe_dev/cctbx.sys_abs_equiv_space_groups -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp cctbx/examples/sys_abs_equiv_space_groups.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm
g++ -o iotbx/detectors/bruker_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/bruker_ext.cpp
g++ -o iotbx/detectors/detectors_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 iotbx/detectors/image_divider.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/image_divider.cpp
g++ -o iotbx/misc/boost_python/dtrek_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/misc/boost_python/dtrek_ext.cpp
g++ -o iotbx/misc/boost_python/scalepack_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/misc/boost_python/scalepack_ext.cpp
g++ -o iotbx/mtz/batch_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/mtz/batch_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/column.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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/mtz/column.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/column_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/mtz/column_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/crystal.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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/mtz/crystal.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/crystal_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/mtz/crystal_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/dataset.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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/mtz/dataset.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/dataset_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/mtz/dataset_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/mtz/ext.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/object.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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/mtz/object.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/mtz/object_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/mtz/object_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/atom_selection.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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/atom_selection.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/common_residue_names_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/common_residue_names_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/construct_hierarchy.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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/construct_hierarchy.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/ext.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hierarchy.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hierarchy_atom_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/hierarchy_atom_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hierarchy_atoms.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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_atoms.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hierarchy_atoms_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/hierarchy_atoms_bpl.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hierarchy_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/hierarchy_ext.cpp
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hierarchy_select.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_atoms.cpp: In function 'std::auto_ptr<iotbx::pdb::hierarchy::atoms::atom_tmp_sentinel> iotbx::pdb::hierarchy::atoms::reset_tmp(const scitbx::af::const_ref<iotbx::pdb::hierarchy::atom>&, int, int)':
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_atoms.cpp:232:44: warning: 'auto_ptr' is deprecated (declared at /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     std::auto_ptr<atom_tmp_sentinel> result(new atom_tmp_sentinel(atoms));
                                            ^
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_atoms.cpp: At global scope:
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_atoms.cpp:243:37: warning: 'auto_ptr' is deprecated (declared at /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     af::const_ref<atom> const& atoms)
                                     ^
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_atoms.cpp: In function 'std::auto_ptr<iotbx::pdb::hierarchy::atoms::atom_tmp_sentinel> iotbx::pdb::hierarchy::atoms::reset_tmp_for_occupancy_groups_simple(const scitbx::af::const_ref<iotbx::pdb::hierarchy::atom>&)':
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/iotbx/pdb/hierarchy_atoms.cpp:245:44: warning: 'auto_ptr' is deprecated (declared at /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/include/g++-v4/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     std::auto_ptr<atom_tmp_sentinel> result(new atom_tmp_sentinel(atoms));
                                            ^
g++ -o iotbx/pdb/hierarchy_write.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/hybrid_36_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/input.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/input_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/input_write.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/overall_counts.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/rna_dna_atom_names_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/utils.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/write_utils.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/pdb/xray_structure_bpl.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o iotbx/shelx/shelx_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/boost_python/slice.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/utils.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o omptbx/stubs.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_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_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_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 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 mmtbx/masks/atom_mask.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 rstbx/dps_core/dps_core.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 rstbx/dps_core/direction.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 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_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_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/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_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 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_symmetry_search_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/symmetry_search/boost_python/symmetry_search_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_covalent_radii_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/covalent_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_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/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_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/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_array_family_flex_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/array_family/boost_python/flex_ext.o cctbx/array_family/boost_python/flex_hendrickson_lattman.o cctbx/array_family/boost_python/flex_miller_index.o cctbx/array_family/boost_python/flex_xray_scatterer.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_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_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/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/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/cctbx_maptbx_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/maptbx/boost_python/maptbx_ext.o cctbx/maptbx/boost_python/grid_indices_around_sites.o cctbx/maptbx/boost_python/grid_tags.o cctbx/maptbx/boost_python/gridding.o cctbx/maptbx/boost_python/misc.o cctbx/maptbx/boost_python/peak_search.o cctbx/maptbx/boost_python/pymol_interface.o cctbx/maptbx/boost_python/statistics.o cctbx/maptbx/boost_python/structure_factors.o cctbx/maptbx/boost_python/coordinate_transformers.o cctbx/maptbx/boost_python/mapper.o cctbx/maptbx/boost_python/basic_map.o cctbx/maptbx/boost_python/real_space_refinement.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_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/cctbx_emma_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/boost_python/emma_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_wavelengths_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/wavelengths_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_neutron_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/eltbx/boost_python/neutron_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_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_eltbx_chemical_elements_ext.so -shared -Wl,-O1 -Wl,--as-needed -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_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_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_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_sgtbx_asu_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp cctbx/sgtbx/direct_space_asu/proto/asu_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lcctbx_sgtbx_asu -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_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_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_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 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/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 rstbx/diffraction/ewald_sphere.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -Wabi -fabi-version=6 -fPIC -fno-strict-aliasing -DNDEBUG -fno-associative-math -ftrapping-math -DBOOST_ALL_NO_LIB -DBOOST_DISABLE_THREADS -ftrapv -march=native -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 mmtbx/bulk_solvent/bulk_solvent.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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_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/dynamics/dynamics_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/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/f_model/f_model_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/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/masks/masks_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/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/ncs/restraints_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/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/rsr/rsr_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_grid.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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_bool.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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_size_t.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_int.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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_long.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_double.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_double_matrix.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
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_complex_double.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_std_string.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_random.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_sort.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_histogram.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_mean_and_variance.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_median.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_linear_interpolation.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_vec3_double.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_vec2_double.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/loops.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/show_sizes.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/array_family/boost_python/shared_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/boost_python/slice_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/iso_surface/iso_surface_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
cc1plus: warning: command line option '-std=gnu11' is valid for C/ObjC but not for C++ [enabled by default]
g++ -o scitbx/linalg/boost_python/linalg_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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 -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
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<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, FloatType&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<int>&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1<bool>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, bool) [with FloatType = double; std::string = std::basic_string<char>]':
/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<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, FloatType&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1<bool>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, bool) [with FloatType = double; std::string = std::basic_string<char>]'
/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<FloatType>::process(const scitbx::af::ref<ElementType>&, const FloatType&, const scitbx::af::ref<ElementType>&, 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<FloatType>::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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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<ElementType>&, 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<char>]':
/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<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, FloatType&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref2<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<int>&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1<bool>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, bool) [with FloatType = double; std::string = std::basic_string<char>]'
/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<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, FloatType&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const FloatType&, const FloatType&, const scitbx::lbfgsb::raw::ref1<ElementType>&, const scitbx::lbfgsb::raw::ref1<int>&, std::string&, const int&, std::string&, const scitbx::lbfgsb::raw::ref1<bool>&, const scitbx::lbfgsb::raw::ref1<int>&, const scitbx::lbfgsb::raw::ref1<ElementType>&, bool) [with FloatType = double; std::string = std::basic_string<char>]'
/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<FloatType>::process(const scitbx::af::ref<ElementType>&, const FloatType&, const scitbx::af::ref<ElementType>&, 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<FloatType>::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: warning: format not a string literal and no format arguments [-Wformat-security]
       printf(fmt_3003);
                      ^
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:971:22: warning: format not a string literal and no format arguments [-Wformat-security]
       printf(fmt_3004);
                      ^
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lbfgsb/raw.h:982:40: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-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: warning: format not a string literal and no format arguments [-Wformat-security]
           if (info == -9) printf(fmt_9019); // itfile
                                          ^
g++ -o scitbx/linalg/boost_python/svd.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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
g++ -o scitbx/linalg/boost_python/eigensystem.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/eigensystem.cpp
g++ -o scitbx/lstbx/boost_python/lstbx_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/lstbx/boost_python/lstbx_ext.cpp
g++ -o lib/scitbx_fftpack_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/fftpack/boost_python/fftpack_ext.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/lib -lomptbx -lscitbx_boost_python -lboost_python-2.7 -lm
g++ -o lib/scitbx_array_family_shared_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/array_family/boost_python/shared_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/lstbx/boost_python/normal_equations.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/lstbx/boost_python/normal_equations.cpp
g++ -o lib/scitbx_lbfgsb_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/lbfgsb/boost_python/lbfgsb_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/math/boost_python/math_ext.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/math_ext.cpp
g++ -o scitbx/math/boost_python/basic_statistics.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/basic_statistics.cpp
g++ -o scitbx/math/boost_python/gaussian.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/gaussian.cpp
g++ -o lib/scitbx_lbfgs_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/lbfgs/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/math/boost_python/golay.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/golay.cpp
g++ -o scitbx/math/boost_python/minimum_covering_sphere.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/minimum_covering_sphere.cpp
g++ -o scitbx/math/boost_python/principal_axes_of_inertia.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/principal_axes_of_inertia.cpp
g++ -o lib/scitbx_linalg_ext.so -shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp -fopenmp scitbx/linalg/boost_python/linalg_ext.o scitbx/linalg/boost_python/matrix.o scitbx/linalg/boost_python/cholesky.o scitbx/linalg/boost_python/householder.o scitbx/linalg/boost_python/svd.o scitbx/linalg/boost_python/eigensystem.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/math/boost_python/row_echelon.o -c -march=native -O2 -g0 -pipe -std=gnu++11 -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 -O2 -g0 -pipe -std=gnu11 -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/math/boost_python/row_echelon.cpp
In file included from /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lstbx/boost_python/normal_equations.cpp:1:0:
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lstbx/normal_equations.h: In instantiation of 'bool scitbx::lstbx::normal_equations_separating_scale_factor<FloatType>::finalised() [with FloatType = double]':
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lstbx/normal_equations.h:248:7:   required from 'void scitbx::lstbx::normal_equations_separating_scale_factor<FloatType>::finalise() [with FloatType = double]'
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lstbx/boost_python/normal_equations.cpp:58:26:   required from 'static void scitbx::lstbx::boost_python::normal_equations_separating_scale_factor_wrapper<FloatType>::wrap(const char*) [with FloatType = double]'
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lstbx/boost_python/normal_equations.cpp:70:9:   required from here
/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r7/work/cctbx_sources/scitbx/lstbx/normal_equations.h:273:14: error: cannot convert 'boost::optional<scitbx::lstbx::normal_equations<double> >' to 'bool' in return
       return reduced_equations_;
              ^
scons: *** [scitbx/lstbx/boost_python/normal_equations.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 3024:  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-r7:20150806-073918.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'