phenix in manjaro round 2

[eva03 /]# cd /usr/local/phenix-dev-2666/build/
[eva03 build]# /usr/local/phenix-dev-2666/base/bin/python /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2666/build --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials xia2 iota prime
Python: 2.7.8 "/usr/local/phenix-dev-2666/base/bin/python"
Compiler: default
Build mode: release
Warning level: 0
Precompiled Headers: False
Static libraries: False
Static exe: False
Scan Boost headers: False
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
Enable OpenMP if possible: False
Boost threads enabled: False
Enable CUDA: False
Use opt_resources if available: False
Use environment flags: False
Enable C++11: False
Force true division: True
command_version_suffix: dev-2666
Relocatable paths anchored at: /usr/local/phenix-dev-2666/build
Top-down list of all modules involved:
  prime              "/usr/local/phenix-dev-2666/modules/cctbx_project/prime"
  iota               "/usr/local/phenix-dev-2666/modules/cctbx_project/iota"
  xia2               "/usr/local/phenix-dev-2666/modules/xia2"
  dials              "/usr/local/phenix-dev-2666/modules/dials"
  xfel               "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel"
  cma_es             "/usr/local/phenix-dev-2666/modules/cctbx_project/cma_es"
  labelit            "/usr/local/phenix-dev-2666/modules/labelit"
  rstbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/rstbx"
  spotfinder         "/usr/local/phenix-dev-2666/modules/cctbx_project/spotfinder"
  annlib+adaptbx     "/usr/local/phenix-dev-2666/modules/annlib"
                     "/usr/local/phenix-dev-2666/modules/annlib_adaptbx"
  phenix             "/usr/local/phenix-dev-2666/modules/phenix"
  reel               "/usr/local/phenix-dev-2666/modules/reel"
  wxtbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/wxtbx"
  phaser             "/usr/local/phenix-dev-2666/modules/phaser"
  phaser_regression  "/usr/local/phenix-dev-2666/modules/phaser_regression"
  tntbx              "/usr/local/phenix-dev-2666/modules/tntbx"
  solve_resolve      "/usr/local/phenix-dev-2666/modules/solve_resolve"
  muscle             "/usr/local/phenix-dev-2666/modules/muscle"
  ksdssp             "/usr/local/phenix-dev-2666/modules/ksdssp"
  pulchra            "/usr/local/phenix-dev-2666/modules/pulchra"
  phenix_html        "/usr/local/phenix-dev-2666/modules/phenix_html"
  phenix_regression  "/usr/local/phenix-dev-2666/modules/phenix_regression"
  elbow              "/usr/local/phenix-dev-2666/modules/elbow"
  Plex               "/usr/local/phenix-dev-2666/modules/Plex"
  PyQuante           "/usr/local/phenix-dev-2666/modules/PyQuante"
  crys3d             "/usr/local/phenix-dev-2666/modules/cctbx_project/crys3d"
  gltbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/gltbx"
  mmtbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/mmtbx"
  suitename          "/usr/local/phenix-dev-2666/modules/suitename"
  king               "/usr/local/phenix-dev-2666/modules/king"
  probe              "/usr/local/phenix-dev-2666/modules/probe"
  reduce             "/usr/local/phenix-dev-2666/modules/reduce"
  iotbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/iotbx"
  cbflib+adaptbx     "/usr/local/phenix-dev-2666/modules/cbflib"
                     "/usr/local/phenix-dev-2666/modules/cctbx_project/cbflib_adaptbx"
  ccp4io+adaptbx     "/usr/local/phenix-dev-2666/modules/ccp4io"
                     "/usr/local/phenix-dev-2666/modules/ccp4io_adaptbx"
  dxtbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/dxtbx"
  smtbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/smtbx"
  ucif               "/usr/local/phenix-dev-2666/modules/cctbx_project/ucif"
  cctbx              "/usr/local/phenix-dev-2666/modules/cctbx_project/cctbx"
  scitbx             "/usr/local/phenix-dev-2666/modules/cctbx_project/scitbx"
  fable              "/usr/local/phenix-dev-2666/modules/cctbx_project/fable"
  omptbx             "/usr/local/phenix-dev-2666/modules/cctbx_project/omptbx"
  boost+adaptbx      "/usr/local/phenix-dev-2666/modules/boost"
                     "/usr/local/phenix-dev-2666/modules/cctbx_project/boost_adaptbx"
  tbxx               "/usr/local/phenix-dev-2666/modules/cctbx_project/tbxx"
  chiltbx            "/usr/local/phenix-dev-2666/modules/cctbx_project/chiltbx"
  libtbx             "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx"
Creating files in build directory: "/usr/local/phenix-dev-2666/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: "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/boost_adaptbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/fable/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/scitbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cctbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/smtbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/dxtbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cbflib_adaptbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/iotbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/reduce/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/probe/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/king/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/suitename/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/mmtbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/gltbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/crys3d/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/elbow/elbow/command_line"
*****************************************************************************************************************************************************************************
WARNING: Ignoring file "relocatable_path(anchor="/usr/local/phenix-dev-2666/build", relocatable="../modules/elbow/elbow/command_line/carbo_load.py.eli")" due to missing "#!"
*****************************************************************************************************************************************************************************
Processing: "/usr/local/phenix-dev-2666/modules/phenix_regression/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/phenix_html/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/ksdssp/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/muscle/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/solve_resolve/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/phaser_regression/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/phaser/phaser/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/wxtbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/reel/reel/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/phenix/phenix/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/spotfinder/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/rstbx/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/labelit/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/ui/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/cxi/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/dials/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/xia2/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/iota/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/prime/command_line"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/scitbx/libtbx_refresh.py"
  Generating C++ header files in:
    "/usr/local/phenix-dev-2666/build/include/scitbx/array_family"
  Generating C++ files in:
    "/usr/local/phenix-dev-2666/build/include/scitbx/array_family/boost_python"
  Using fable to convert scitbx/lbfgs.f
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cctbx/libtbx_refresh.py"
  Generating C++ files in:
    "/usr/local/phenix-dev-2666/build/cctbx/eltbx"
  Generating C++ files in:
    "/usr/local/phenix-dev-2666/build/include/cctbx/boost_python"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/smtbx/libtbx_refresh.py"
  Generating C++ files in:
    "/usr/local/phenix-dev-2666/build/include/smtbx/boost_python"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py"
  Copying to lib: "/usr/local/phenix-dev-2666/modules/cbflib/pycbf/pycbf.py"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/iotbx/libtbx_refresh.py"
  Using fable to convert iotbx/pdb/hybrid_36_f.f
    Writing: iotbx/pdb/hybrid_36_fem.cpp
Processing: "/usr/local/phenix-dev-2666/modules/reduce/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/probe/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/mmtbx/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/gltbx/libtbx_refresh.py"
  Generating C++ files in:
    "/usr/local/phenix-dev-2666/build/gltbx"
      Info: Re-using existing font cpp files.
      Hint: Remove gltbx/FONTS_UCS_DONE_FLAG_FILE
            to force generation of new font files.
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/crys3d/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/phenix_regression/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/solve_resolve/libtbx_refresh.py"
  Number of hpp files generated from resolve cpp files: 720
Processing: "/usr/local/phenix-dev-2666/modules/phenix/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/annlib_adaptbx/libtbx_refresh.py"
  Generating C++ files for self-inclusive approximate nearest neighbor
Processing: "/usr/local/phenix-dev-2666/modules/cctbx_project/xfel/libtbx_refresh.py"
Processing: "/usr/local/phenix-dev-2666/modules/dials/libtbx_refresh.py"
Cleaning up 'dials/extensions':
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/median_background_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/null_background_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/gmodel_background_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/simple_background_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/kabsch_spotfinder_threshold_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/simple_centroid_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/gaussian_rs_profile_model_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/glm_background_ext.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/__init__.pyc
 Deleting /usr/local/phenix-dev-2666/modules/dials/extensions/helen_spotfinder_threshold_ext.pyc
Violación de segmento (`core' generado)